AFNI HISTORY
level 2 and higher
The levels of importance go from 1 to 5, with meanings:
1 - users would not care
2 - of little importance, though some users might care
3 - fairly important
4 - a big change or new program
5 - IMPORTANT: we expect users to know
generated via the command : afni_history -html -reverse -min_level 2
---- log of AFNI updates (most recent first) ----
17 Dec 2024, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add a simple convolve function
17 Dec 2024, RC Reynolds, Makefile.linux_ubuntu_24_ARM, level 2 (MINOR), type 2 (NEW_OPT)
duplicate the 24_64 Makefile but with the ARM system name
10 Dec 2024, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_modulator_stats option, showing min,mean,max,stdev stats
06 Dec 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
subtract 1 from ricor QC vrat, for more a useful display
Previously output ratio of orig/ricor variances to view improvement.
Subtract 1 for better visualization, since the orig ratio must be > 1,
leaving the image as a more direct 'fractional improvement', say.
Or equivalently, call it (orig-ricor)/ricor.
17 Nov 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
add -make_flags option
11 Nov 2024, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_tr_offset_stats
This enhances -show_tr_stats, and might replace it.
A start to what was requested by Gang.
23 Oct 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -volreg_no_volreg
Replace the 3dvolreg alignment transformation with the identity.
The B Feige option.
10 Oct 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
mask intersect inputs did not have views
Thanks to martinsingua on the MB for pointing out the problem.
04 Oct 2024, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 2 (NEW_OPT)
add -datatable 'command', to generate table for R stats programs
Use gen_group_command.py -command datatable to generate datatable files
for -dataTable options, for programs like 3dMVM, 3dLME, etc.
24 Sep 2024, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 4 (BUG_FIX)
fix confusion over auto-gzip BRIK name
19 Sep 2024, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
allow use of build_afni.py for updating the current package
If build_afni.py was used to create the current package, then @uab
will also use it for updating (rather than downloading an official
package. One can also specify to use it via -build_afni.
16 Sep 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
if which Xvfb fails, check for its existence on disk
Also, include .login and report fewer homebrew link suggestions.
16 Sep 2024, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
apply LOCAL_CC_PATH in Makefile.macos_13_ARM and Makefile.macos_12_x86_64
13 Sep 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in eispack C files, include math.h before f2c.h
This should generally have no effect, since the local f2c.h
includes math.h. However, if one is using cmake and the system
f2c for linking (rather than using afni/src/f2c), then the f2c.h
included with the eispack files will not have math.h.
So locally include math.h, just to be sure.
12 Sep 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE)
add option -cc_path
Allow one to pass an alternate compiler if the relevant Makefile
uses LOCAL_CC_PATH. If this option is not used and the default
compiler does not exist, try to find the most recent similar version.
11 Sep 2024, P Taylor, gtkyd_check, level 2 (MINOR), type 7 (REMOVE)
Remove the *tcsh script* version of gtkyd_check.
This has now been superseded by a Python version of same name.
10 Sep 2024, P Taylor, gtkyd_check, level 3 (MAJOR), type 1 (NEW_PROG)
A *Python* version of previously-written tcsh script of same name.
Much faster way of checking/tabulating a glob of datasets for properties.
04 Sep 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 5 (MODIFY)
use uname -m for CPU, instead of platform.processor()
04 Sep 2024, RC Reynolds, OS_notes.macos_12_b_user.tcsh, level 2 (MINOR), type 6 (ENHANCE)
allow the script to be re-run with no effect
30 Aug 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
many updates to help examples; separate paths in compare_opts
- make example option order more consistent
- add examples: publish 3e ... 3j
- exclude 'noshow' examples from default help (currently 3e,f,g,h,j)
- separate differing paths in -compare_opts
05 Aug 2024, RC Reynolds, compute_ROI_stats.tcsh, level 2 (MINOR), type 5 (MODIFY)
if ALL_LT includes an ROI value of zero, remove it
05 Aug 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add option -blip_warp_dset to input a pre-computed warp
For example, one can import the warp from epi_b0_correct.py.
23 Jul 2024, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
undo the the problematic -f change from 2024/04/26
The -f was added to tcsh to prevent biowulf from updating the PATH
when using whereami, as they have a different program with that name.
But -f means that on macs DYLD vars would not be set, crashing afni
when using the macos_10.12_local binaries.
25 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
deal with -Wimplicit-int, mostly from old f2c, needed for gcc-14
24 Jun 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE)
when running 'make', warn if CC is set (which usually causes failure)
24 Jun 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
display CC; warn if CPU type differs between platform and uname
20 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
stop reporting assuming TR=1.0 warnings for now
Requested by P Taylor.
20 Jun 2024, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
make -read_all the default
Basically for real-time sorting, this forces the initial processing
of all (found) images, rather than a limited subset. It allows for
proper sorting without requiring an initial alphabetical aspect.
14 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
AFNI.afnirc : use GZIP compression and turn off obliquity warnings
AFNI_COMPRESSOR : default to GZIP
AFNI_AUTOGZIP : comment out (was YES)
AFNI_NO_OBLIQUE_WARNING : default to YES
AFNI_ONE_OBLIQUE_WARNING : comment out (was YES)
11 Jun 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
backup directory removal; add -update_niivue option
Save only most recent backup directory, possibly plus 1 containing afni.
Add -update_niivue, and skip the operation on '-clean_root no'.
06 Jun 2024, RC Reynolds, rPkgsInstall, level 2 (MINOR), type 5 (MODIFY)
along with 3dMVM, handle not having afni in PATH
06 Jun 2024, RC Reynolds, Makefile.macos_13_ARM, level 2 (MINOR), type 2 (NEW_OPT)
add this Makefile (in src) for corresponding build machine
This is a ~dupe of other_builds/Makefile.macos_13_ARM_clang.
30 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
remove unimportant anat followers from example 'publish 3d'
30 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix volreg TSNR for ME: use eind -> fave_echo
Thanks to zhengchencai on MB for pointing out the problem.
25 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -bids_deriv option
This adds a call to P Taylor's map_ap_to_deriv.py program, to output a
BIDS derivative tree.
25 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -volreg_allin_warp option
This allows specific control over 3dAllineate -warp, using a default
of shift_rotate for rigid body registration.
24 May 2024, PD Lauren, suma, level 3 (MAJOR), type 2 (NEW_OPT)
add alpha thresholding
29 Apr 2024, RC Reynolds, afni-general, level 3 (MAJOR), type 5 (MODIFY)
change 'count' program and usage to 'count_afni'
Add count_afni to the distribution, modify scripts to use it, and
allow use of count_afni is sub-brick selection, e.g.,
dset'[count_afni 3 5]'
Note that 'count' is still allowed, for now.
26 Apr 2024, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
-init_uvars_json will now pass through unknown uvars
This enables users to pass uvars through afni_proc.py to the APQC.
26 Apr 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in any script calling whereami, invoke with 'tcsh -f' at top
This is a quick fix for biowulf usage, since there is a new whereami
in town (/usr/local/bin/whereami), and because they reset the PATH.
Modify: @Atlasize @MakeLabelTable @chauffeur_afni
compute_ROI_stats.tcsh gen_cluster_table
25 Apr 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
warn if tcsh version is 6.22.03 - it has $var:h bug
25 Apr 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -uvar option to pass through AP uvars
24 Apr 2024, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -sort_method geme_suid
22 Apr 2024, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
singleton coordinates should round to the closest voxel center
Originally, box coordinates rounded to the nearest voxel, effectively
extending ranges by 1/2 voxel on each side. This was changed in 2021 to
be strict. But then singleton coordinates often hit no voxels, and the
help says one voxel should be found.
Now a singleton coordinate will round to the nearest center, while a ':'
separated range will be precise, as with the mixed use:
-xbox 5.4:11.3 -17.8:-4.1 11
Here, the '11' will be rounded to the closest center.
17 Apr 2024, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
in THD_load_nifti(), need_copy might imply scale_data
Thanks to @liningpan on github for reporting this.
12 Apr 2024, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 2 (NEW_OPT)
add -label_prefix, to include labels in the output prefix
08 Apr 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -anat_follower_erode_level, to specify the exact erosion level
The older -anat_follower_erode option implies only a single erosion.
This parameter is in voxels. As before, a single erosion includes the
18 NN2 neighbors, so all in a 3x3x3 box but the outer 8 corners.
See mask_tool -help for details.
Added for M. Byrne S. Haller.
07 Apr 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
the default warp vox dim will round up if very close
Particularly when coming from a NIFTI sform, voxel dimensions are often
computed. So while an "exact" dimension might be 3, the computed one
might come out as 2.99999. Scale dimensions by 1.0001 before truncation.
05 Apr 2024, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
add reg_echo and echo_times; include echo_times in basic review script
29 Mar 2024, RC Reynolds, ap_run_simple_rest_me.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
run a quick afni_proc.py resting state analysis for QC on multi-echo data
29 Mar 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add 'none' as an option to -regress_apply_mot_types
This allows one to censor (or compute enorm) without motion regression.
Requested by e0046902 on NeuroStars.
29 Mar 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
NIFTI s/qform_code of 2 defaults to +orig, once again
Have an unset AFNI_NIFTI_VIEW default to 'orig' again.
This is how it was originally. It was changed at some point to
accommodate an influx of such data in MNI space. Now, revert to
having sform_code of 2 to default to orig space.
28 Mar 2024, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY)
temporarily revert to 2023.1003 SUMA tree, while fixing some issues
Most of this will go back in, once the issues are resolved.
22 Mar 2024, RC Reynolds, 2dImReg, level 2 (MINOR), type 6 (ENHANCE)
add approx_equal() test for -basefile, as well
Done for josef_ling on MB.
21 Mar 2024, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 6 (ENHANCE)
allow 'column' label ANY, which expands to each non-initial label
21 Mar 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -disp_abin
21 Mar 2024, P Taylor, gtkyd_check, level 2 (MINOR), type 1 (NEW_PROG)
Add new program to make summaries of data file properties.
Glob many datasets, get tables to compare for similarities/diffs.
20 Mar 2024, RC Reynolds, 2dImReg, level 2 (MINOR), type 6 (ENHANCE)
be more lenient, not requiring dx to be exactly equal to dy
Done for josef_ling on MB.
18 Mar 2024, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
auto-include APQC_atlas for compute_tsnr_stats, if appropriate
And add -regress_compute_auto_tsnr_stats.
15 Mar 2024, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
add rt.06.ME.OC.aves example, like 05 but with ROI averages
12 Mar 2024, RC Reynolds, SUMA, level 2 (MINOR), type 4 (BUG_FIX)
updates to SUMA_CreateDO.c, SUMA_Color.c, SUMA_driver.c
Some build machines need to adhere to the C99 standard.
11 Mar 2024, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
add max_4095_warn_dset key and driver use
11 Mar 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add 4095_gcount warnings for input EPI
This will be automatically run after the outlier counts.
08 Mar 2024, RC Reynolds, 3dTto1D, level 2 (MINOR), type 6 (ENHANCE)
add 4095_gcount warning method; modify output
Zero out results if max is not exactly 4095.
05 Mar 2024, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
add Optimally Combined multi-echo demo, including use with afni_proc.py
04 Mar 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add -disp_ver_afni (display contents of AFNI_version.txt)
01 Mar 2024, RC Reynolds, compute_ROI_stats.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add ability to pass ALL_LT via -rval_list (for all labeltable entries)
29 Feb 2024, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY)
use raw straing format for some regular expressions
So python 3.12 has upgraded Deprecation Warnings to SyntaxWarnings,
making warnings pop up where they did not previously. Previously, one
would need to turn on deprecation warnings to see such things.
28 Feb 2024, RC Reynolds, module_test_lib.py, level 2 (MINOR), type 6 (ENHANCE)
python 3.12 has removed 'imp' importing library, use importlib
Add a new 312 function string for newest case.
22 Feb 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE)
check for conda env vars on make build failure
22 Feb 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
check for conda env vars
22 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
use more mask_epi_anat, and default: -regress_compute_tsnr_stats brain 1
21 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 2 (MINOR), type 5 (MODIFY)
modify labels and prep for Q column
15 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
compute per-ROI region statstics over a given dataset
It is a little like 3dROIstats, but with needs specific to afni_proc.py.
15 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -regress_compute_tsnr_stats
This is intended to be added to P Taylor's APQC HTML report.
08 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
in radcor: pass mask after any data scaling or in regress block
Scaled or errts data won't automask well.
Also, block radcor once in the surface domain.
07 Feb 2024, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 6 (ENHANCE)
add regress to -radial_correlate_blocks
Also, handle new DEFAULT example names, and pass using underscores.
05 Feb 2024, RC Reynolds, @FindAfniDsetPath, level 2 (MINOR), type 5 (MODIFY)
one change to allow spaces in dataset names
Spaces in the paths to templates/atlases or the abin is currently
not allowed. But we might slowly change that.
02 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -ROI_import (in prep for TSNR stats)
01 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
-show_example_keywords, -show_pythonic_command; revamp examples
21 Jan 2024, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT)
add -wrap_text and -wrap_text_method for more clear command line use
21 Jan 2024, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY)
redo deep PT special
18 Jan 2024, RC Reynolds, 3dZeropad, level 2 (MINOR), type 2 (NEW_OPT)
add options -pad2odds, -pad2mult (pad to any positive multiple)
Motivated by P Taylor.
11 Jan 2024, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
validate fim_now in AFNI_autorange_label
If the underlay existed in both orig and tlrc view, switching to the
view without an overlay would cause a crash.
Thanks to msh23m (AFNI message board) for noting the problem.
08 Dec 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 4 (BUG_FIX)
copy README files into build_src; use prev directory, not prefix
Thanks to D Glen for noting the missing README files.
07 Dec 2023, RC Reynolds, @update.afni_binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -overwrite_build
This option is now required to allow @uab to run and overwrite
a local binary package that was created using build_afni.py.
04 Dec 2023, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
allow more n/a fields in tsv files
27 Nov 2023, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
add some comments about build_afni.py
24 Nov 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add -disp_ver_pylibs
Show python library __version__ strings.
Check for flask and flask_cors with -check_all.
20 Nov 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
add 'rsync_preserve' backup_method; rsync now cleans abin after backup
Prior to this, abin was allowed to accumulate files. That is no longer
the default operation.
14 Nov 2023, RC Reynolds, 3dNLfim, level 2 (MINOR), type 4 (BUG_FIX)
when creating non-bucket output, if float output, make all volumes float
Thanks to V Dinh for noting the problem.
30 Oct 2023, RC Reynolds, Makefile.macos_13_ARM_clang, level 2 (MINOR), type 5 (MODIFY)
(w/DG) use homebrew gcc-13, and downgrade -O2 to -O1
We have yet to resolve why /usr/bin/gcc led to a 3dSkullStrip crash.
And brew gcc-13 led to a 3dvolreg crash, but that seems to be due to
failed compiler optimizations. Using -O1 works.
12 Oct 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 5 (MODIFY)
only require flat_namespace if 10.12_local or 10.7_local
10 Oct 2023, RC Reynolds, init_user_dotfiles.py, level 2 (MINOR), type 5 (MODIFY)
allow -do_updates to override all updates from -test
10 Oct 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 5 (MODIFY)
require -build_root; tail build errors; default to atlas updating
28 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -disp_R_ver_for_lib
28 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
split OS_notes_macos_12 by CPU
Now have : OS_notes.macos_12_{ARM,intel}_a_admin.zsh
and : OS_notes.macos_12_{ARM,intel}_b_user.tcsh
The b_user scripts still just run OS_notes.macos_12_b_user.tcsh.
26 Sep 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
install NiiVue; add option -update_atlases, to download newest package
21 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
capture the platform of the R version
18 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -use_asc_path, to test using directory of afni_system_check.py
15 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
have all R wrapper scripts (scripts_for_r) return the status from R
To match returning non-zero when loading R_io.so.
13 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
create OS_notes.macos_12_b_user.tcsh to be an executable install script
Have OS_notes.macos_12_x86_64_b_user.txt just execute the new script.
Reluctantly done to appease D Glen (thanks).
13 Sep 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
have 1d_tool.py -write_xstim create an empty file if empty matrix
This got lost, but is needed for @ss_review_basic on rest data.
08 Sep 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
new operation: by default, back up and install the build results
This is a change in behavior. Upon a successful build, default is now
back up the ABIN and install new binaries and atlases.
Add options -abin, -do_backup, -do_install, -backup_method.
07 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
change afni/build to afni_build in OS_notes.macos_12_x86_64_b_user.txt
Thanks to spartaaa-git@github.com for pointing that out.
01 Sep 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_slice_timing_gentle
Also, use mean timing diff rather than median.
28 Aug 2023, RC Reynolds, test_afni_prog_help.tcsh, level 2 (MINOR), type 6 (ENHANCE)
rename from test.afni.prog.help and moved to scripts_install
This is now distributed for more general testing.
21 Aug 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
apply uncensored TRs via a text file rather than command line
With a long encoded TR list, file names might exceed the allowable limit
(currently about 5100 bytes), e.g. data+tlrc'[3,5..7,10..13,23]'.
Instead, use the 1dcat functionality to get those volume indices from
a text file. So if trs.txt contains 3 5 6 7 10 11 12 13 23,
then one can read the volumes using data+tlrc'[1dcat trs.txt]'.
Thanks to G Edwards and S Japee for diagnosing the issue.
17 Aug 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -slice_pattern_to_times
Output timing given known to3d tpattern, nslices, multiband level, and TR.
17 Aug 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
rewrite -show_slice_timing_pattern
Be more forgiving in timing when trying to detect a pattern.
08 Aug 2023, RC Reynolds, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
when creating bucket output, clear time dimension
Thanks to Philip on MB for noting the problem.
27 Jul 2023, RC Reynolds, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
distribute niiview as niiview_afni.umd.js
This is intended to be used via P Taylor's APQC HTML report.
Requested by P Taylor.
26 Jun 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
write NIFTI-2 if dimensions require it
14 Jun 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
default to -radial_correlate_blocks errts, if none given
08 Jun 2023, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 6 (ENHANCE)
add build maker to AFNI_version.txt
07 Jun 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
start looking for dependent libraries (under linux for now)
Also, rearranged some of the output.
Done at the behest of P Taylor.
02 Jun 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -regress_errts_prefix for surface analysis
It was missing $hemi to specify the hemisphere.
Thanks to A Gilemore for bringing up the issue.
10 May 2023, RC Reynolds, Makefile.macos_12_x86_64, level 2 (MINOR), type 2 (NEW_OPT)
add Makefile, updates, and OS_notes
27 Apr 2023, RC Reynolds, Isosurface, level 2 (MINOR), type 4 (BUG_FIX)
include updates for the 2002.08.12 MarchingCubes code base
Thanks to C Rorden for providing an updated translation.
20 Apr 2023, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
sync with NIFTI-Imaging/nifti_clib
19 Apr 2023, RC Reynolds, APMULTI_Demo1_rest, level 2 (MINOR), type 6 (ENHANCE)
add do/run_40* scripts
These are in the apmulti_scripts repo.
14 Apr 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
add Makefile.linux_rocky_8 and OS_notes.linux_rocky_8.txt
These should work on RHEL/CentOS/Rocky/Almalinux 8.
This is now a new build package.
06 Apr 2023, P Taylor, afni_util.py, level 2 (MINOR), type 0 (GENERAL)
Add new functions for shell_com logging (kind like history ).
write_afni_com_log(), proc_log(), format_log_dict().
06 Apr 2023, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL)
Add new attribute/methods for shell_com logging (kinda like history).
save_log, add_to_log, shell_log, etc.
03 Apr 2023, RC Reynolds, @diff.tree, level 2 (MINOR), type 6 (ENHANCE)
update @diff.tree, @diff.files: possibly switch to meld if no xxdiff
Be automatic, rather than forcing one to use '-diff_prog meld'.
03 Mar 2023, P Taylor, auto_warp.py, level 2 (MINOR), type 2 (NEW_OPT)
Put in -hview functionality, to show full help.
Running with no opts will also show FULL help (not annoying short one!).
01 Mar 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_pretty_command, to print a more readable one
Append this to a current command to generate prettier one, not to run it.
27 Feb 2023, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -choose_nonzero_cols
This is to exclude all-zero columns for condition number of chosen cols.
27 Feb 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_indices_allzero
List indices of all-zero coluns.
19 Feb 2023, RC Reynolds, build_afni.py, level 3 (MAJOR), type 1 (NEW_PROG)
compile AFNI
- download from github
- download AFNI atlases
- compile
- suggest rsync (will apply with some options, later)
17 Feb 2023, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
when counting events, default (with GUESS) to GLOBAL
Previously, when the user did not specify either -local_times or
-global_times, the number of events (and therefore IM regressors)
was based on local time run length, so many event regressors might
not be included.
Change the default to be based on -global_times.
If IM, warn if the user did not specify the timing type.
Thanks to M Hoptman for letting us know of the problem.
06 Feb 2023, RC Reynolds, init_user_dotfiles.py, level 2 (MINOR), type 6 (ENHANCE)
add -shell_list and prep for possible librification
06 Feb 2023, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
show multiband level and timing patternn in basic output
06 Feb 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
include output from init_user_dotfiles.py -test
06 Feb 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
propagate slice_pattern from any -tshift_opts_ts -tpatttern
04 Feb 2023, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add timing_to_slice_pattern() - to determine known slice time patterns
04 Feb 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_slice_timing_pattern
03 Feb 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
actually fail (not just warn) on inconsistent num echoes
Thanks to T Weiss bringing up the issue.
01 Feb 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
get SurfSmooth params from smrec dset
Thanks to Erin G for bringing up the issue.
24 Jan 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add QC output to ricor block
24 Jan 2023, RC Reynolds, 3dvolreg, level 2 (MINOR), type 6 (ENHANCE)
add error message for trimming weight set to empty
For now, still let it crash. Try to trap in startup_lsqfit later.
17 Jan 2023, P Taylor, 3dAutobox, level 2 (MINOR), type 6 (ENHANCE)
And just like that, update/improve the ijkord functionality and format.
Also explain more clearly what is happening in a help section.
17 Jan 2023, P Taylor, 3dAutobox, level 2 (MINOR), type 2 (NEW_OPT)
More new options, in particular for ijkord (-> useful for 3dcalc expr).
Also clean up other features/help. Add -npad_safety_on, too.
10 Jan 2023, P Taylor, convert_cdiflist_to_grads.py, level 2 (MINOR), type 6 (ENHANCE)
Output more information if the input cdiflist appears to be ragged.
Help pinpoint the potential problem row for the user.
06 Jan 2023, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 2 (NEW_OPT)
Add '-vstat_list' opt, so user can enter label bases for vstat in APQC.
HTML still has up to 5 automatically chosen vols by def in vstat.
03 Jan 2023, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -write_tsv_cols_of_interest with -tsv_labels
23 Dec 2022, RC Reynolds, init_user_dotfiles.py, level 3 (MAJOR), type 1 (NEW_PROG)
evaluate or initialize dot/RC files for running AFNI
From the perspective of:
i) adding a directory (ABIN?) to the PATH
ii) sourcing the apsearch all_progs.COMP file (per shell)
iii) (for macs) adding flat_namespace to DYLD_LIBRARY_PATH
02 Dec 2022, P Taylor, @animal_warper, level 2 (MINOR), type 6 (ENHANCE)
Add another QC image if '-init_scale ..' is used.
Useful to check if scaling is approximately appropriate.
01 Dec 2022, P Taylor, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT)
Opt '-init_scale ..' to provide initial len scaling before affine align.
Useful if input is much smaller/bigger than template.
23 Nov 2022, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add add -align_unifize_epi local and -compare_to options
23 Nov 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add examples simple_rest_QC, simple_rest_QC_na
These are the DEFAULT comparison example in ap_run_simple_rest.tcsh.
23 Nov 2022, P Taylor, find_variance_lines.tcsh, level 2 (MINOR), type 6 (ENHANCE)
Put a backslash before shell commands, so possible aliases aren't used.
Also put numbers by each exit. Thanks, S Torrisis!
15 Nov 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -find_var_line_blocks for calling find_variance_lines.tcsh
14 Nov 2022, RC Reynolds, find_variance_lines.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
(w PT/DG) look for columns of high temporal variance in time series
Will be a recommended QC option in afni_proc.py.
09 Nov 2022, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-weight_corr ..' (diff application than '-weight_ts ..').
Calculate weighted Pearson Correlation. For Dante P.
02 Nov 2022, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -sort_method case geme_xnat
Sort as with geme_index, but pre-sort with RIN rather than alphabetical.
13 Oct 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix crash (in afni_base.py) if missing template
Thanks to R Birn for noting the problem.
13 Oct 2022, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
add -no_hist to 3dinfo, to omit the HISTORY text
12 Oct 2022, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
add basic output of 'final DF fraction'
08 Oct 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
w/PT, reformat help examples and remove extra indentation
05 Oct 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 6 (ENHANCE)
Output a run_instacorr_errts.tcsh script in the results directory.
Very useful for data QC. Use it. Quick now, here, now, always...
22 Sep 2022, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-clusterize_wami ..', for Clustering functionality.
Adds a 'whereami' table to the output dir.
02 Sep 2022, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
trap NIFTI write errors (via new nifti_image_write_bricks_status())
Have 3dcopy and 3dreit return non-zero status on failure.
Thanks to J Teves for reminding us of this shortcoming.
30 Aug 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
make -show_example allow unique substring matching
This allows one to run simply 'afni_proc.py -show_example 6b', say.
Also, pass final_epi_dset as a uvar when there is no warped version.
30 Aug 2022, P Taylor, abids_json_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
Add -values_stay_str flag, so num/str items stay as str type.
Otherwise, by default they attempt to be int, then float, then str.
30 Aug 2022, P Taylor, abids_json_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
Add -literal_keys flag, to turn off auto-replacement of spaces and [()].
Also try to keep ints looking like ints.
18 Aug 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 6 (ENHANCE)
Display final EPI coverage mask on final space dset.
Could be on template, final anatomical or vr_base.
17 Aug 2022, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 6 (ENHANCE)
use of -anat is now optional, only -epi is needed
12 Aug 2022, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
add Makefile.linux_ubuntu_22_ARM_clang, as written by C Rorden
Thanks to C Rorden for submitting the file.
11 Aug 2022, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-button_press ..', for Norm/Colr/Swap buttons.
Adds in functionality from driving AFNI GUI.
09 Aug 2022, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
modify how censor dset is applied in get_max_displacement
30 Jul 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
copy tlrc_base/template to results dir; add opt -tlrc_copy_base
Done for QC and visualization purposes; requested by P Taylor.
29 Jul 2022, RC Reynolds, afni_base.py, level 2 (MINOR), type 5 (MODIFY)
update locate() : return 1 if found, even via @Find
28 Jul 2022, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE)
add -Wl,-headerpad_max_install_names to linker command
Make space for install_name_tool -change to use @executable_path.
Thanks to witherscp on MB for noting the problem.
26 Jul 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
when warping an anat follower, if appropriate, copy the label table
Done at the behest of the mighty P Taylor.
04 Jul 2022, P Taylor, 3dLocalUnifize, level 2 (MINOR), type 2 (NEW_OPT)
Well, a new arg for '-local_mask ..' opt.
Use arg value 'None' to turn off the default automasking now.
17 Jun 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 2 (NEW_OPT)
add and apply nifti_image_write_status in NIFTI-1 and -2
06 Jun 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -align_unifize_epi local method, -align_opts_eunif
To apply 3dLocalUnifize from P Taylor.
06 Jun 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Add new ve2a QC, via new uvar final_epi_unif_dset.
Also scale ulay=EPI brightness better for EPI-to-anat align imgs.
06 Jun 2022, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT)
Some new opts to control ulay brightness, esp. for APQC HTML.
New opts: '-ulay_range_am ..' and '-ulay_min_fac ..'
06 Jun 2022, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Some new opts to control ulay brightness, esp. for APQC HTML.
New opts: '-ulay_range_am ..' and '-ulay_min_fac ..'
03 Jun 2022, P Taylor, 3dLocalUnifize, level 2 (MINOR), type 1 (NEW_PROG)
New program for unifizing brightness.
Should be helpful for alignment.
24 May 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -command_comment_style
As requested by the ominous P Taylor.
17 May 2022, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 2 (NEW_OPT)
add to prog lists
11 May 2022, P Taylor, SurfLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
The 'mean' stat was accumulating int, not float, values.
This effective truncation/'digitizing' error should be fixed now.
10 May 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
do not add global line wrapper to QC block
Avoid line wrappers in the generation of out.ap_uvars.txt (might happen
when copy_anat dset has a very long name, for example).
Thanks to E Chang for pointing out the issue.
06 May 2022, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add functions slice_pattern_to_order, slice_pattern_to_timing
03 May 2022, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
for anyos_* packages, test for update using AFNI_version.txt
02 May 2022, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
add distribution packages anyos_text and anyos_text_atlas
29 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
prepare for the all-important anyos_text distribution
Add Makefile.anyos_text and an install_text target in Makefile.Include.
29 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
apply PRId64 for some int64_t printing
Modified niml.h, niml_elemio.c, mri_transpose.c, thd_loaddblk.c.
28 Apr 2022, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX)
afni_util.py:common_dir() : watch for the deadly JR scenario!
Thanks to J Ritchie for unconvering this, peculiar, issue.
27 Apr 2022, RC Reynolds, Makefile.macos_11_ARM_clang, level 2 (MINOR), type 5 (MODIFY)
(w/dglen) modify recent mac builds to get all X packages from homebrew
Modified Makefile.macos_11_ARM_clang, Makefile.macos_10.15_clang, and
the corresponding other_builds/OS_notes files.
23 Apr 2022, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT)
Can specify which shell to use, because there are newer shell(s).
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
23 Apr 2022, P Taylor, @afni_refacer_make_master_addendum, level 2 (MINOR), type 0 (GENERAL)
Now creates a v2.0 of the shell.
The new shell removes more face. Asked for by A. Basavaraj.
22 Apr 2022, RC Reynolds, Dimon, level 3 (MAJOR), type 2 (NEW_OPT)
add -sort_method cases rin and geme_rin
22 Apr 2022, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
add -no_frivolities option, to directly set that
22 Apr 2022, P Taylor, afni, level 2 (MINOR), type 4 (BUG_FIX)
The '-bysub ..' opt wasn't working, because a 'find' cmd was bad.
Reformatted the 'find', though it might still benefit from other tweaks.
14 Apr 2022, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 4 (BUG_FIX)
Replacement was not occurring if ROIs were purged by modal smoothing.
Fixed that bug, hopefully improving robustness to such error in future.
12 Apr 2022, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
add Makefile.linux_fedora_35_shared and OS_notes.linux_fedora_35.txt
06 Apr 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow for REML-only errts on surface
Thanks to P Molfese for bringing it up.
05 Apr 2022, RC Reynolds, 3dTshift, level 2 (MINOR), type 6 (ENHANCE)
allow for shifting a single slice (or voxel) time series
Also, add a help example demonstrating this.
01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT)
Add '-disp_def_params' so the user can see the default params.
The params will also now get displayed during runtime.
01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT)
Add many more '-min_* ..' options for controlling badness criteria.
Asked for by user nseider: hope these are helpful!
01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 5 (MODIFY)
Actually output the number of bad slices per volume.
Previously had some ~fancy encoding about criterion of badness (why?).
01 Apr 2022, P Taylor, 3dZipperZapper, level 2 (MINOR), type 2 (NEW_OPT)
New opts '-dont_use_*' to turn off some of the drop criteria at will.
Also put in help descriptions about drop criteria, in Notes.
22 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add ap_uvars dir_suma_spec, suma_specs
Also, remove inappropriate -epi_strip from -align_opts_aea in example.
16 Mar 2022, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -show_tr_offsets
See Example 10 d.
15 Mar 2022, RC Reynolds, afni_util.py, level 2 (MINOR), type 4 (BUG_FIX)
cast run_time_to_polort output to int, for py2.7
Thanks to P Taylor for pointing it out.
12 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
use aea.py instead of allin for extra -align_epi_ext_dset registration
align_epi_anat.py would deal with a difference in obliquity
10 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
run 3dAllineate for -align_epi_ext_dset to volreg base
09 Mar 2022, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Patch unfathomable problem with -permute and -covariates combined
Covariate matrices are constructed BEFORE permutation is setup, and
that caused a problem. Patched around that.
08 Mar 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
apply -polort in @radial_correlate
07 Mar 2022, RC Reynolds, @radial_correlate, level 2 (MINOR), type 2 (NEW_OPT)
add -polort; default is 2
02 Mar 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
sync with nifti_clib repo
01 Mar 2022, RC Reynolds, nifti_tool, level 3 (MAJOR), type 2 (NEW_OPT)
allow conversion between any 2 int or float types (except float128)
Add -copy_image, -convert2dtype, -convert_verify, -convert_fail_choice.
Conversion operations happen in nt_image_read and nt_read_bricks,
and can therefore be applied to most data-included operations.
Requested by J Teves.
20 Feb 2022, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
sync with nifti_clib
18 Feb 2022, RC Reynolds, @Install_APMULTI_Demo2_realtime, level 3 (MAJOR), type 1 (NEW_PROG)
new install script for APMULTI_Demo2_realtime
This is a demo for running AFNI's real-time system, without needing to
bother the scanner. It demonstrates use if single- and multi-echo
DICOM input, and various sets of data that can be passed from afni to
an external program (realtime_receiver.py in this case).
16 Feb 2022, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
propagate obliquity in case of -ftype AFNI
16 Feb 2022, P Taylor, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
Add opt '-compressor ..' so AFNI_COMPRESSOR env var can be set.
Leads to created *.BRIK dsets getting compressed on disk.
14 Feb 2022, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_keepers
Show table of subjects kept, rather than those with any outliers.
Added on the authority of P Taylor.
12 Feb 2022, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT)
3dMean can compute max, min, absmax, signed_absmax
3dMean keeps only one dataset in memory at a time
and can process thousands of datasets. These options
emulate the options across time in 3dTstat
10 Feb 2022, RC Reynolds, afni_python_wrapper.py, level 2 (MINOR), type 4 (BUG_FIX)
change import to try from afnipy first
Biowulf has old afnipy/*.py files in abin.
Thanks to P Kusmierek and P Taylor for reporting the problem.
09 Feb 2022, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix FIR blur padding
As noted by PT, volumes were not being properly blurred near edges.
Fix edge padding to be applied for entire FIR length, not just at
full FIR offset.
08 Feb 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -html_review_opts for passing options to apqc_make_tcsh.py
Done for S Torrisi.
08 Feb 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 2 (NEW_OPT)
AP now can pass some '-html_review_opts ..' values to this prog.
First one: '-mot_grayplot_off', for envelope-pushing user S Torrisi.
07 Feb 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
create out.ap_uvars.json, and apply via gssrs -init_uvas_json
A minor assist in helping P Taylor take over this spiral galaxy arm...
07 Feb 2022, P Taylor, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Add a new stat: MCONEX, the Michelson Contrast of Extrema.
mconex = |A-B|/(|A|+|B|), where A=max and B=min.
06 Feb 2022, P Taylor, 3dedgedog, level 2 (MINOR), type 0 (GENERAL)
If -only2D opt is used, then don't blur in 3D, either.
Also turn off optimized double blurring---essentially not time diff.
06 Feb 2022, P Taylor, 3dedgedog, level 2 (MINOR), type 4 (BUG_FIX)
Fix some badness when 4D datasets are input.
Also have a better scale value, based on 3dLocalstat sigma.
03 Feb 2022, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT)
add -init_uvas_json
Allow passing a json file, akin to passing many -uvar options.
29 Jan 2022, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
add -extras_on_one_line
To display any 'extra' values using only one line, per TR.
27 Jan 2022, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -write_sep, -write_style, to control format of output
26 Jan 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Update QC block: vorig now shows the epi-anat overlap.
Shows overlap with ignoring obliquity and applying it (if present).
26 Jan 2022, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 4 (BUG_FIX)
Fix how -box_focus_slices opt works if one of the AMASK* keywords is used.
Previously was producing error, not recognizing it wasn't a dset.
25 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Update QC block: vorig now shows the 'copy_anat' dset.
Applies in all cases; AP just passes along uvar. Thanks, RCR!
25 Jan 2022, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 2 (NEW_OPT)
Add in existing chauffeur options: -no_cor, -no_axi, -no_sag.
For APQC---vorig of initial overlap.
24 Jan 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
pass combine_method to gen_ss_review_scripts.py
This will be applied to the 'mecho' APQC section by P Taylor.
20 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Update QC block: vstat (for task-based FMRI cases).
There will now be typically up to 5 stats dsets shown (GLT and other).
18 Jan 2022, RC Reynolds, @Install_APMULTI_Demo1_rest, level 3 (MAJOR), type 1 (NEW_PROG)
(w/PT) new install script for APMULTI_Demo1_rest
This is a demo for running various multi-echo processing methods
on resting state data via afni_proc.py.
(renamed from @Install_AP_MULTI_DEMO1)
18 Jan 2022, RC Reynolds, 3dDiff, level 2 (MINOR), type 5 (MODIFY)
remove declarations after statements and init any free'd pointers
18 Jan 2022, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Add a new QC block: mecho.
This is for multi-echo (ME) FMRI; mostly for m_tedana right now.
18 Jan 2022, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL)
New functions/functionality for the new QC block: mecho.
Also tweaked/updated the help.
13 Jan 2022, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Do a check if the user asks for 'pythonic' APQC.
If their system CAN'T HANDLE THE TRUTH, then downgrade kindly to 'basic'.
12 Jan 2022, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL)
got rid of remaining uninit warnings (even if code was okay)
12 Jan 2022, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 4 (BUG_FIX)
Add '-save_ftype ..' opt to this script, to make @animal_warper happy.
Thanks, DRG, for pointing this out.
12 Jan 2022, P Taylor, 3dDepthMap, level 2 (MINOR), type 0 (GENERAL)
Rename program: 3dEulerDist -> 3dDepthMap.
The original name was odd for *Euclidean* Distance Transform, anyways...
11 Jan 2022, RC Reynolds, tedana.py, level 2 (MINOR), type 5 (MODIFY)
even without -seed, always apply a seed (default = 42)
Now 2 executions should produce the same result, unless -seed is
modified. This matches the MEICA group tedana.
11 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
add option -disp_ver_matplotlib
Done under the now-even-more-strict-than-before orders from P Taylor.
11 Jan 2022, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
rename -combine_method m_tedana_tedort to m_tedana_m_tedort
Reserve the former for future tedort projection via AFNI.
11 Jan 2022, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
if missing, init .afnirc/.sumarc
10 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
matplotlib is required ; check version >= 2.2
05 Jan 2022, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
check for having both .cshrc and .tcshrc
29 Dec 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -write_simple_tsv
Also, read and write default mod_* modifier columns.
29 Dec 2021, P Taylor, 3dedgedog, level 2 (MINOR), type 0 (GENERAL)
Change default sigma_rad to be 1.4, not 2.0, to capture more details.
This is because results look much better in human T1w dset.
26 Dec 2021, P Taylor, 3dedgedog, level 2 (MINOR), type 2 (NEW_OPT)
The -automask (and -automask+X) functionality is now, well, functional.
The '-mask ..' option appears to be working, too.
26 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 0 (GENERAL)
Give correct name of opt in prog help: -bounds_are_not_zero.
Had forgotten the '_not' part previously. Whoops.
24 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 2 (NEW_OPT)
Can process some dsets much faster now, with opt '-binary_only'.
This is to flag that the input is a binary mask.
19 Dec 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
misc updates for circleCI build based on xcode 12.4.0
Remove thd_incorrelate.o from cmake libmri, etc.
19 Dec 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_distmat
Display nrows x nrows matrix of distances between all vector row pairs.
Option added for jkblujus (AFNI MB).
15 Dec 2021, RW Cox, prefiltered args, level 2 (MINOR), type 2 (NEW_OPT)
Bulk input arguments
These '<
09 Dec 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
balls were not verified to be entirely within dset bounds
Thanks to aclyn11 (AFNI MB) for noting the problem.
09 Dec 2021, RC Reynolds, 3dinfo, level 2 (MINOR), type 5 (MODIFY)
further restrict -same_center
Change def limit from 0.1*sum_vox_diags to 0.001*ave_vox_diag.
08 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 0 (GENERAL)
Already change something internally about only2D calcs.
Should just be simple change, being more general.
08 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 2 (NEW_OPT)
Can run in 2D now, with opt '-only2D ..'.
For Daniel Glen.
03 Dec 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -combine_method m_tedana_tedort
Now have MEICA group tedana methods:
m_tedana, m_tedana_OC, m_tedana_tedort
01 Dec 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 4 (BUG_FIX)
Was getting incorrect voxel scaling along a couple axes---fixed now.
Also re-arrange functions to be easier to call from other funcs.
30 Nov 2021, P Taylor, 3dEulerDist, level 2 (MINOR), type 1 (NEW_PROG)
New C prog for Eulerian Distance Transform (EDT) for ROI-based dsets.
Calculate distances to boundaries within a FOV.
24 Nov 2021, RC Reynolds, 3dmaskdump, level 2 (MINOR), type 4 (BUG_FIX)
make boxes tight; scale radius to voxel counts
Tighten boxes and balls to not include unrequested voxels.
Scaling the radius allows for sub-mm voxels.
21 Nov 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add updates for current tedana; add -help_tedana_files
15 Nov 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
pull THD_nifti_process_afni_ext() out of thd_niftiread.c:THD_open_nifti()
This should have no effect.
It is preparation for testing the AFNI extension in NIFTI against dset.
07 Nov 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -regress_opts_fwhmx (for adding options to 3dFWHMx)
Added on the authority of S Torrisi.
29 Oct 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
on mac, check for standard R not in PATH
29 Oct 2021, P Taylor, @Install_NMT, level 2 (MINOR), type 0 (GENERAL)
Update macaque template+atlas data.
Now working/defaulting to NMT v2.1.
29 Oct 2021, P Taylor, @Install_MACAQUE_DEMO_REST, level 2 (MINOR), type 0 (GENERAL)
Update macaque demo for resting state FMRI processing.
New scripts, now working/defaulting to NMT v2.1.
27 Oct 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
try to warn on insufficient disk space
Check if any data partition has less than 5 GB available.
Done to appease the mighty P Taylor.
27 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Opt '-extra_qw_opts ..' had wrong name in help file, '-qw_opts ..'.
Corrected this, as well as usage.
25 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Improve QC outputs, and fix some chauffeur ranges.
Hopefully easier to evaluate alignment now, among other features.
23 Oct 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
For ROI image QC, use ROI_glasbey_2048 now by default.
CHARM has ROI values >256, so might as well go all in.
21 Oct 2021, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
allow for previously set DYLD_LIBRARY_PATH
20 Oct 2021, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 6 (ENHANCE)
do not allocate errts/fitts on -x1D_stop
08 Oct 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -show_xmat_stype_cols
Display xmat columns for specified -stim_* regressor classes.
02 Oct 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
Copy input anat (and any mask_ss) into the output directory.
Can be useful for checking if things went awry (do they ever?!?).
01 Oct 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -show_xmat_stim_info
Display xmat info for -stim_* regressor classes.
29 Sep 2021, P Taylor, 3dAllineate, level 3 (MAJOR), type 0 (GENERAL)
3dAllineate: set -lpa+ to re-include 'ov' in its recipe---for stability.
This makes it closer to historical form (but no 'mi' still).
29 Sep 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL)
Just running '-help' leads to lesion_outs.txt to be created and populated.
... and it also got overwritten oddly. Move those lines further down.
29 Sep 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior with longnames---just needed a quote around var.
Should work now. Also update help.
27 Sep 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_INSTACORR_JUMP
If YES (default), Shift+Ctrl+click sets the instacorr seed and jumps the
crosshairs to that location. If NO, sets the instacorr seed but there is
no crosshair jump. (For Phil Kohn)
27 Sep 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_imit2w_from_t1w, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_decmap, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_convert_dcm_anat, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @djunct_4d_imager, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @afni_refacer_run, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
27 Sep 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
On/about Aug 23, 2021, default label_sizes in image windows changed.
That shrunk fonts down one size; now bump back up @chauffeur_afni calls.
23 Sep 2021, P Taylor, @epi_b0_corr.py, level 2 (MINOR), type 2 (NEW_OPT)
Had been missing the internal processing of option '-epi_pe_bwpp'.
... which has now been added in.
23 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Can now perform clusterizing, with Alpha+Boxed on, like in GUI.
New opt '-clusterize ..' for some commands; see help/NOTES for full info.
21 Sep 2021, RC Reynolds, 3dTshift, level 2 (MINOR), type 6 (ENHANCE)
propagate toffset, if not zero
21 Sep 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 2 (NEW_OPT)
Add in new opts to turn off images in particular view planes being made.
These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC.
21 Sep 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 2 (NEW_OPT)
Add in new opts to turn off images in particular view planes being made.
These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC.
21 Sep 2021, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT)
Add in new opts to turn off images in particular view planes being made.
These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC.
21 Sep 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Add in new opts to turn off images in particular view planes being made.
These are '-no_cor', '-no_axi', '-no_sag'. First will help APQC.
20 Sep 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL)
apsearchize.
Make help visible in editor with '@grayplot -hview'.
20 Sep 2021, P Taylor, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT)
Add '-raw_with_bounds ..' to display raw values in arbitrary interval.
Maybe most useful if data have been scaled.
31 Aug 2021, RW Cox, 3dTcorr1D/3dTcorrelate, level 2 (MINOR), type 4 (BUG_FIX)
Change labels and statcode for -Fisher option
Sir Paul pointed out that these programs didn't have the correct
statcode when the Fisher transform was ordered, and also that the labels
were confusing. Fixed it so if -Fisher was used, the statcode is FIZT vs
FICO, and the labels have 'atanh()'
31 Aug 2021, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add option -gert_chan_digits, to specify num digits for channel in name
31 Aug 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL)
Change default cost function to 'lpa', from 'ls'.
Should be better? There is an opt to change, as necessary.
30 Aug 2021, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
New opts: '-all_roi_zeros' and '-automask_off'.
Basically, N ROIs can have NxN mat, even if ROI ave is all zeros.
20 Aug 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -write_tsv_cols_of_interest
17 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 6 (ENHANCE)
Modified to use OpenMP
3dTfitter.c, thd_fitter.c, and thd_lasso.c
10 Aug 2021, RW Cox, 3dTfitter, level 2 (MINOR), type 1 (NEW_PROG)
Add -LCB option for block-wise LASSO penalties
LCB = LASSO Centro Block
The penalty in a block is
sum{ ABS[ beta[i] - centromean(beta[i],...) ] }
which is intended to make all the beta[i] in a block shrink towards a
common value, rather than towards 0. The intent is to use this with IM
regression models from 3dDeconvolve, to reduce outliers in the
stimulus-wise beta estimates.
10 Aug 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 5 (MODIFY)
No longer worry about even/odd slice output (and remove '-no_fs_prep').
Dealt with an old non-issue.
29 Jul 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 2 (NEW_OPT)
Add in @chauffeur_afni functionality: -edgy_ulay.
27 Jul 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix typo in cubic resampling for viewer/3dresample (afni_slice.c)
Done with P Taylor.
27 Jul 2021, P Taylor, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix typo in cubic resampling for viewer/3dresample (afni_slice.c)
Copying Rick's fix. Thanks to user 'ymao' for raising this issue on the MB
.
26 Jul 2021, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
add options -dcx, -dcy, -dcz, dc3
This provides the center of the volumetric grid, in DICOM coords.
22 Jul 2021, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -multi_durations_from_offsets
Added on the authority of W-L Tseng.
20 Jul 2021, RW Cox, NIML library, level 3 (MAJOR), type 4 (BUG_FIX)
NIML file: input failed if file over 2BG in size
Due to storing filesize in int/long. Fix was to make it stored in
int64_t, and fixing a few other places.
15 Jul 2021, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT)
add -empty_is_outlier, to treat empty fields as outliers
The default reporting of blank outlier test vals is now as non-outliers.
Use this option to report as outliers.
Added for the mighty P Taylor.
09 Jul 2021, P Taylor, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT)
New: '-aff_move_opt ..' to use more than just giant_move in aff step.
Also bug fix for when no followers were entered.
30 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
Tweak column names *again*.
Add in extra check that 3D vols are specified (e.g., with selectors).
29 Jun 2021, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT)
-log2 and -log10 options
To convert statistics to minus the logarithm of p-value.
28 Jun 2021, RW Cox, NIML, level 2 (MINOR), type 4 (BUG_FIX)
Change byte count output for NI_write_element to int64_t
And a few other functions as well. Reason: someone tried to create a 2.8
GB .niml.dset file, which caused a problem when counting up the bytes
output using a 32 bit int. Users -- what can you do with them?
28 Jun 2021, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
Reformat report*.1D tables a bit: match key and col names.
Also, improve/simplify/clarify names of cols. Thanks, Adam Messinger.
28 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Well, OK, not *really* a new opt---new values accepted for existing opt.
The '-olay_alpha ..' can now take Linear or Quadratic (grazie, Bob).
25 Jun 2021, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
add -rand_post_elist_partition
This will partition an already defined stim class into new ones.
Added on the authority of S Haller.
24 Jun 2021, P Taylor, @djunct_overlap_check, level 2 (MINOR), type 0 (GENERAL)
Silence 3drefit warns if changing space of dsets (might confuse users).
Unnecessary warning for these temp dsets within the script.
22 Jun 2021, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
calm those grumpy compilers
Issues noted by P Taylor.
22 Jun 2021, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY)
without -datum, the output now depends on the map func, not the BRIK
Done to appease the mysterious D Glen.
22 Jun 2021, P Taylor, SurfLayers, level 2 (MINOR), type 0 (GENERAL)
Capture verbose output from ConvertSurface.
Also add -no_clean opt.
22 Jun 2021, P Taylor, 3dNwarpCalc, level 2 (MINOR), type 0 (GENERAL)
Put in std includes to be able to build on Mac with Clang.
Though this program isn't even built...
21 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 5 (MODIFY)
Change default blok type and radius for the lpc/lpa methods
Old default was -blok 'RHDD(6.54321)'.
New default is -blok 'TOHD(0)' where the 0 radius means to compute the
blok radius so as to give the blok a volume of 555 times the volume of a
base dataset voxel. For 1x1x1 voxels, such as the MNI template, this
results in 'TOHD(5.18)'. If users want the old setup, they'll have to
use the old blok definition explicitly.
18 Jun 2021, P Taylor, @Install_SURFLAYERS_DEMO1, level 2 (MINOR), type 0 (GENERAL)
Created by Sam Torrisi. Help added, temp placeholder data now in place.
Will add full demo data soon...
18 Jun 2021, P Taylor, @Install_AP_MULTI_DEMO1, level 2 (MINOR), type 0 (GENERAL)
Adding install script for afni_proc.py multi-echo FMRI demo (OHBM, 2021).
Demo authors: RC Reynolds, SJ Gotts, AW Gilmore, DR Glen, PA Taylor.
15 Jun 2021, P Taylor, lesion_align, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_imit2w_from_t1w, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_decmap, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_convert_dcm_anat, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, ap_run_simple_rest.tcsh, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @update.afni.binaries, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @toMNI_Qwarpar, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @toMNI_Awarp, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @simulate_motion, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fix (never hit?), and avoid single line 'if' conds.
Latter to avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @radial_correlate, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @parse_name, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @parse_afni_name, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @move.to.series.dirs, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @measure_in2out, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @measure_erosion_thick, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @measure_bb_thick, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @grayplot, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @global_parse, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @get.afni.version, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @fix_FSsphere, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @djunct_slice_space, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @djunct_glue_imgs_vert, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @diff.tree, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @diff.files, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @compute_gcor, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @clip_volume, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @clean_help_dir, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @build_afni_Xlib, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @afni_refacer_make_onebigA12, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @afni_refacer_make_master, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @afni.run.me, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @T1scale, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @ScaleVolume, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_Make_Spec_SF, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_Make_Spec_Caret, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL)
Clean up some spacing; avoid single line 'if' conds; use unaliased rm.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SUMA_AlignToExperiment, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @RetinoProc, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @Reorder, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @ROI_decluster, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @MakeLabelTable, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @Install_InstaCorr_Demo, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @Install_ClustScat_Demo, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @GradFlipTest, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @FS_roi_label, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @ExamineGenFeatDists, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @Atlasize, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @AddEdge, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if'.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @2dwarper.Allin, level 2 (MINOR), type 0 (GENERAL)
Avoid single line 'if' conds.
To avoid badness in some (older?) tcsh versions.
15 Jun 2021, P Taylor, @1dDiffMag, level 2 (MINOR), type 0 (GENERAL)
Put spaces in if-conditions after 'if' and before 'then'.
To avoid badness in some (older?) tcsh versions.
14 Jun 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Space before 'then' in if-cond; also remove all exclamations in comments.
Resolved *very* weird opt parsing on *some* old tcsh.
10 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
rename src/suma_suma.h to src/SUMA/SUMA_X_objs.h
This is to avoid glorious case-insensitive name conflicts on Macs.
As suggested by the merciful D Glen.
10 Jun 2021, RC Reynolds, SurfLocalstat, level 2 (MINOR), type 1 (NEW_PROG)
add Ziad's program to the default build
This is to allow use of the 'mode' stat.
09 Jun 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 6 (ENHANCE)
Changes to make T1-T1 alignment with lpa+ZZ more reliable
Problem - aligning whole head volume to MNI template (top of head only)
- alignment sometimes fails badly. This problem is much less common if
source and base image coverage are compatible. If users will not zero
out or chop off the sub-brainstem part of the head, then the following
changes made to 3dAllineate will help:
a) carry out a larger search in the coarse pass (more trials)
b) eliminate 'ov' and 'mi' from lpa+ as these caused problems
NOTE: 'ov' and 'mi' are still in lpc+
Also investigated why linux and macos results differ. Tracking optimizer
leads to hypothesis that differences in roundoff error slowly
accumulate, and then at some point powell_newuoa makes a step decision
that can alter the optimizing trajectory significantly. There doesn't
seem to be a good way to avoid this. However, with the chanes above,
both macos and linux versions work reasonably well, and differ at most
in about 2 mm (and that only in one case out of 38 whole head tests).
03 Jun 2021, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 6 (ENHANCE)
sync crorden/dcm2niix_console with repo, version v1.0.20210317
Thanks to C Rorden for suggesting the update.
02 Jun 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL)
Undo previous tweak to auto_warp.py; back to using *.nii.
Reverting, because AFNI_COMPRESSOR has been updated.
01 Jun 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
AFNI_COMPRESSOR no longer affects NIFTI (seems AFNI_AUTOGZIP never did)
30 May 2021, P Taylor, auto_warp.py, level 2 (MINOR), type 0 (GENERAL)
Use *.nii.gz, not *.nii, because of current AFNI_COMPRESSOR = GZIP.
With current AFNI_COMPRESSOR = GZIP, get problems; now, no more.
30 May 2021, P Taylor, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT)
New opt '-use_gz' to output gzipped NIFTI even with '-suffix ..'.
Part of updating auto_warp.py to use *.nii.gz, not *.nii.
24 May 2021, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL)
Several small updates for convenience and organization: help updated...
more QC images; split intermediate text desc; new cmd_log.
17 May 2021, DR Glen, lesion_align, level 3 (MAJOR), type 1 (NEW_PROG)
Alignment for data with large lesions
Developed for hemispherectomy and lobectomy data.
May be applicable to stroke and smaller lesion data too
06 May 2021, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE)
Make -zskip work with -paired
Rejecting any value pairs where either setA or setB is 0.
01 May 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix niml.dset suffix in the case of -regress_compute_fitts on the surface
Thanks to the all-seeing S Torrisi for noting the problem.
29 Apr 2021, P Taylor, 3dClusterize, level 2 (MINOR), type 2 (NEW_OPT)
Forgot to actually add in the new opt for data scaling in last change...
Now opt '-abs_table_data' is in the code.
29 Apr 2021, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
1) Now apply any scaling to 'data' in table (wasn't scaling, before).
2) Change table def: don't abs val Mean and SEM; use opt for that.
23 Apr 2021, P Taylor, 1dplot.py, level 2 (MINOR), type 2 (NEW_OPT)
Can force ylabels to wrap at a certain num of chars (-ylabels_maxlen ..).
For APQC, so long stimulus labels don't run into each other.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 7 (REMOVE)
This program has been superseded by: adjunct_apqc_tsnr_general.
The new version is more... general.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 7 (REMOVE)
This program has been superseded by: adjunct_apqc_tsnr_general.
The new version is more... general.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 2 (NEW_OPT)
More options from @chauffeur_afni here.
Tryin' to make nicer images.
16 Apr 2021, P Taylor, adjunct_apqc_tsnr_general, level 2 (MINOR), type 1 (NEW_PROG)
Made to replace adjunct_apqc_tsnr_with_mask and adjunct_apqc_tsnr_no_mask.
Also expands/generalizes this functionality.
06 Apr 2021, RC Reynolds, ap_run_simple_rest.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
run a quick afni_proc.py resting state analysis for QC
24 Mar 2021, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
-FWHMxyz allows different blurring amounts in different directions
24 Mar 2021, P Taylor, 3dBrickStat, level 3 (MAJOR), type 4 (BUG_FIX)
Fix bug: having non-full-FOV mask + perc calcs affected other calcs.
Calcs should now be consistent even with those opts used. Thanks, RCR.
16 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
simplify logic in THD_mask_erode(), with negligible slowdown
15 Mar 2021, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT)
add convenience options -perclist and -perc_quiet
13 Mar 2021, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE)
distribute libXp.6.dylib, since XQuartz has stopped doing it
Thanks to C Gaillard and others on the MB.
10 Mar 2021, RC Reynolds, lib_tsv.py, level 2 (MINOR), type 1 (NEW_PROG)
new TSV class library, geared toward BIDS event files
10 Mar 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 2 (NEW_OPT)
Add in more control features, so can apply in more cases.
Basically just allowing more chauffeur control.
08 Mar 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applying NIFTI scale_slope to dset must be after setting ADN_datum
Previously, NIFTI scalars were applied only after a DSET_load().
Thanks to D Glen for reporting the issue.
06 Mar 2021, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL)
Run a bit more quietly, setting ENV vars and GUI opts.
Fewer warnings and messages.
06 Mar 2021, P Taylor, @fat_tract_colorize, level 2 (MINOR), type 0 (GENERAL)
Run a bit more quietly, setting ENV vars and GUI opts.
Fewer warnings and messages. And tweak help to be more useful.
06 Mar 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL)
Run a bit more quietly, setting ENV vars and GUI opts.
Fewer warnings and messages.
05 Mar 2021, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -show_cormat_warnings_full
This version includes the baseline terms in the warning list.
05 Mar 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Have APQC copy the ss_review_basic text file into the QC dir.
Might want this text info available for easy parsing at group level.
04 Mar 2021, RC Reynolds, 3dROIstats, level 2 (MINOR), type 4 (BUG_FIX)
fix surprising slowness
This would previously unload/mallocize/reload every time point,
possibly to free completed data. Then NIFTI input would be re-read
every time point (this might have changed due to something else).
Instead, mallocize in the first place, not per time point.
Also, avoid scaling floats by 1.0.
Thanks to C Craddock for reporting the problem.
03 Mar 2021, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY)
update dotfiles for 'complete' files before running apsearch
Do this so apsearch will not tell users to update the dotfiles again.
Thanks to D Glen.
03 Mar 2021, RC Reynolds, @clean_help_dir, level 2 (MINOR), type 5 (MODIFY)
warn on any error in 'cat *.complete* > xx' commands
In MacOS 11 Rosetta terminals, those commands are *sometimes* crashing.
Warn on any such failure.
Such a crash could cause trouble for other programs, too.
Thanks to D Glen.
03 Mar 2021, P Taylor, gen_ss_review_scripts.py, level 2 (MINOR), type 0 (GENERAL)
Add sswarper2 to name of recognized progs for getting template dset.
Can get uvar for APQC for this top secret NL alignment prog.
03 Mar 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 4 (BUG_FIX)
Had an early exit from earlier debugging.
Ironic, really, that a debugging line became a bug. Go figure.
03 Mar 2021, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 4 (BUG_FIX)
On one system an instrutable error message 'Unknown user: 1~.' occurred.
This change (doublequote file name? remove EOL in backticks?) fixed it.
03 Mar 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE)
Make nice new WB mask, make some QC images of mask/segs/ROIs.
Also make tables of ROI info (size stuff).
01 Mar 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Fix output dir of an intermediate QC image.
The init*uaff* should now be in the usual QC/ dir.
27 Feb 2021, DR Glen, clang macos 11 M1-ARM mods, level 3 (MAJOR), type 0 (GENERAL)
Makefile changes for ARM builds for new Macs
Makefile, misc. changes for building for M1
25 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
With non-nonlinear warps, processing now goes all they way through.
Bit more *.txt output, fixed mapping of anat follower non-ROI dset.
24 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -regress_extra_ortvec, -regress_extra_ortvec_labels
Pass sets of regressors of no interest, to go into the baseline.
Requested by multiple people, including Carolin31 on MB.
24 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Add more TSNR plotting: if vreg TSNR is calc'ed, or if no mask exists.
Also a bug fix in HAVE_MASK definition; fix ranges in some plots.
24 Feb 2021, P Taylor, adjunct_apqc_tsnr_no_mask, level 2 (MINOR), type 1 (NEW_PROG)
Now used in APQC to make TSNR plot.
Has mostly required olay/ulay args, for when *no* mask exists.
22 Feb 2021, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
masking is no longer applied to TSNR dset; pass mask_dset to gen_ss
Requested by P Taylor.
22 Feb 2021, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
New part of regr block: TSNR plot.
Shows brain slices.
22 Feb 2021, P Taylor, adjunct_apqc_tsnr_with_mask, level 2 (MINOR), type 1 (NEW_PROG)
Now used in APQC to make TSNR plot.
Has mostly required olay/ulay args, as well as mask.
22 Feb 2021, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: -pbar_comm_gen, for APQC.
Also remove warning about ffmpeg unless using MPEG.
19 Feb 2021, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY)
updates for ShowMode in SUMA_xColBar.c
Resolve compiler warnings, but avoid logic changes at the same time
as XQuartz beta issues. So temporarily keep original logic.
Once we feel stable with XQuartz, look into expected fixes.
Search for 'todo: apply ShowMode' in SUMA_xColBar.c.
18 Feb 2021, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
warn about problematic version of XQuartz
Bad versions seem to be 2.8.0_alpa*, 2.8.0_betas[12] (3+ okay?).
With improvements we have seen, maybe we should warn on any beta.
17 Feb 2021, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
moved AFNI_ijk_* protos from afni.h to 3ddata.h
All thd_coords.c protos are in 3ddata.h now.
10 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL)
More QC images: WM and GM tissue, solo.
Thanks for suggestions, P Molfese.
10 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
Add in -mask_ss option, to replace skullstripping with a mask.
For example, using fs*mask*nii from @SUMA_Make_Spec_FS after FS.
09 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 0 (GENERAL)
Add fractional volume info to the text file.
This makes 2 new columns in the output *.1D files.
09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL)
New column of ROI vol fraction, relative to fs_parc_wb_mask.nii.gz.
This prog should always be run after adjunct_suma_fs_mask_and_qc.
09 Feb 2021, P Taylor, adjunct_suma_roi_info, level 2 (MINOR), type 0 (GENERAL)
Renamed, from adjunct_suma_rois_qc.tcsh.
Removing extension.
09 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 0 (GENERAL)
Make new mask dset from parcellation.
Add new image of new dset.
09 Feb 2021, P Taylor, adjunct_suma_fs_mask_and_qc, level 2 (MINOR), type 0 (GENERAL)
Renamed, from adjunct_suma_fs_qc.tcsh.
Removing extension.
08 Feb 2021, P Taylor, adjunct_suma_rois_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG)
Will add to @SUMA_Make_Spec_FS for automatic QC output.
This makes *.1D files of voxel counts of parcellations and segs.
08 Feb 2021, P Taylor, adjunct_suma_fs_qc.tcsh, level 2 (MINOR), type 1 (NEW_PROG)
Will add to @SUMA_Make_Spec_FS for automatic QC output.
This makes images of the brain mask, tissue segs and parcellation.
07 Feb 2021, DR Glen, clang+gcc10 macos 10.15 mods, level 3 (MAJOR), type 4 (BUG_FIX)
Lots of little code fixes to handle compiler warnings
Makefile updated and some long outstanding issues fixed
05 Feb 2021, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
Add in more intermediate QC snapshots (intermed align): init*jpg
Also add '-echo' opt for verbose terminal stuff.
03 Feb 2021, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
New QC image, of affine warping.
Also pass along '-echo' opt to modal smoo/report script.
01 Feb 2021, P Taylor, 3dedge3, level 2 (MINOR), type 2 (NEW_OPT)
Adding -automask (and -automask+X) functionality.
Mainly to help with comparisons with 3dedgedog.
27 Jan 2021, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE)
New run script created (run_01*) in L_MAKE_DRIVE_SCRIPT block.
Opens std.141*both*spec in SUMA and SurfVol in AFNI, and starts talking.
27 Jan 2021, P Taylor, 3dAttribute, level 2 (MINOR), type 0 (GENERAL)
Update help to have fancy sections and more examples.
Also provide link to README.attributes file, for user reference.
26 Jan 2021, RW Cox, 3dAllineate, level 2 (MINOR), type 2 (NEW_OPT)
New -PearSave option
Saves the local Pearson correlations into a dataset at the end of an
alignment. Mostly for visualization fun.
26 Jan 2021, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
do not convert NIFTI scaled shorts to float
If slope!=0 && inter==0, pass slope as brick_fac.
Thanks to C Caballero and S Moia for reporting this.
11 Jan 2021, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE)
AFNI graph viewer box labels now selectable from menu
In the Colors, Etc. menu, new items were added to enable and control the
labels used in Box mode. Keystroke ctrl-B cycles between all Data modes.
In addition, labels can now be drawn for graph matrix size up to 9x9.
03 Jan 2021, RC Reynolds, SurfMeasures, level 2 (MINOR), type 5 (MODIFY)
shift memory allocation/free around, mostly to match libSUMA
Inspired by C Rorden via sanitizer warnings.
29 Dec 2020, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
sync with nifti_clib
22 Dec 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed 6 copy-and-paste errors using MRI_TYPE_maxval
Thanks to C Rorden for bringing this up and suggesting code fixes.
22 Dec 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
New default feature_size: 0.5. (Old default: was unset).
Made almost no dif in mac demo, but should be slightly more robust, in gen
.
22 Dec 2020, P Taylor, 3dmaskave, level 2 (MINOR), type 4 (BUG_FIX)
MRI_TYPE_maxval fixed for byte case-- thanks, C Rorden!
Same fix applied in: plug_maskave.c and thd_makemask.c.
21 Dec 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
The '-orient ..' opt wasn't working-- that has been fixed.
Now user can specify table coords with this opt.
01 Dec 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
Tweaked default temp 'junk' filename to avoid low-probability badness
New opt '-tmp_name_nice' for, well, read opt name. Improved help, too.
06 Nov 2020, P Taylor, adjunct_tort_read_dp_align.py, level 2 (MINOR), type 1 (NEW_PROG)
Script to read TORTOISE-DIFFPREP *_transformations.txt files.
Puts them into usable order for calc'ing enorm and plotting mot/pars.
06 Nov 2020, P Taylor, adjunct_tort_plot_dp_align, level 2 (MINOR), type 1 (NEW_PROG)
Script (tcsh) to translate TORTOISE-DIFFPREP *_transformations.txt files
Wraps new adjunct_tort_read_dp_align.py and 1dplot* to make plots.
02 Nov 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL)
Can now output SVG files, and can use newline chars in labels.
Had to deal with newline escape seq internally.
28 Oct 2020, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 0 (GENERAL)
Extra QC image: initial overlap of source and base dsets.
Should help to know, in case anything goes awry later.
28 Oct 2020, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 0 (GENERAL)
Extra QC image: initial overlap of T1w and T2w dsets.
Should help to know, in case anything goes awry later.
19 Oct 2020, P Taylor, @djunct_overlap_check, level 3 (MAJOR), type 1 (NEW_PROG)
Make of overlap of 2 datasets (esp for pre-align check, AW or SSW).
Will make both non-obl and 3dWarp-deob'ed images of olap (and report).
19 Oct 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL)
Simplifying output dir: Phase II and III. Thanks again, B Jung!
New intermediate dir, animal_outs update, helpfile rewritten.
19 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Added new QC image to QC/ dir: initial source-base alignment.
If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report.
19 Oct 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
Added new QC image: initial source-base alignment (@djunct_overlap_check)
If obl, make 1 img ignoring it, and 1 3dWarp-deob'ed, with text report.
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Simplifying output dir: Phase I. Thanks, Ben Jung, for good suggestions!
Put report*1D in QC/, and do*.tcsh and surfaces_* in new surfaces/ dir.
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Add in status checks after many afni progs, to exit at/near first failure.
Should be no change in output for users (in successful runs).
16 Oct 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Now, first cp+resample src to RAI; else, shft is bad for non-xyz orients.
Output warps can still apply to original orient dset fine.
24 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
Put in status checks through script to exit with error if any step fails.
Should provide nicer behavior if something gang agley.
17 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX)
fix use of platform.mac_ver (was there a change?)
15 Sep 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
whine if .zshrc references all_progs.COMP.bash; backup for distro
14 Sep 2020, RC Reynolds, apsearch, level 2 (MINOR), type 6 (ENHANCE)
create complete.zsh files - like bash ones, but cleaned a little
14 Sep 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
update .zshrc: set PATH and DYLD_L_P..., and source all_progs.COMP.zsh
10 Sep 2020, DR Glen, Driving AFNI to get values, level 2 (MINOR), type 6 (ENHANCE)
Drive AFNI to get current value in OLay, Threshold or ULay+
Can also get ULay and OLay prefixes
02 Sep 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
add options -show_field and -show_field_names
Using the new -show_field option, for each entry one can show:
- the full entry (as before)
- only the first/main line
- only the program name, or date, or author, etc.
02 Sep 2020, P Taylor, @SkullStrip_TouchUp, level 2 (MINOR), type 0 (GENERAL)
Replace '-e' at top with several later status checks; 'exit 0' after help.
No effect on output, except being more general.
01 Sep 2020, P Taylor, fat_roi_row.py, level 2 (MINOR), type 6 (ENHANCE)
Update to run in Python 3 (using 2to3, plus extra tweaks).
Should now run in both Python 2 and 3.
01 Sep 2020, P Taylor, fat_proc_grad_plot, level 2 (MINOR), type 7 (REMOVE)
Remove program from distribution.
Already have a better one (with fewer dependencies!) ready to go.
01 Sep 2020, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 6 (ENHANCE)
Update to run in Python 3 (using 2to3, plus extra tweaks).
Should now run in both Python 2 and 3.
01 Sep 2020, P Taylor, fat_mvm_review.py, level 2 (MINOR), type 7 (REMOVE)
Remove program from distribution.
This program never even made it to full beta status.
01 Sep 2020, P Taylor, fat_mvm_prep.py, level 2 (MINOR), type 6 (ENHANCE)
Update to run in Python 3 (using 2to3, plus extra tweaks).
Should now run in both Python 2 and 3.
01 Sep 2020, P Taylor, fat_mvm_gridconv.py, level 2 (MINOR), type 6 (ENHANCE)
Update to run in Python 3 (using 2to3, plus extra tweaks).
Should now run in both Python 2 and 3.
01 Sep 2020, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 6 (ENHANCE)
Update to run in Python 3 (using 2to3, plus extra tweaks).
Should now run in both Python 2 and 3.
01 Sep 2020, P Taylor, fat_lat_csv.py, level 2 (MINOR), type 7 (REMOVE)
Remove program from distribution, with lib: lib_fat_Rfactor.py.
R deps are a mess between Py2 and Py3; might rewrite better in future.
01 Sep 2020, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX)
If '-skipwarp' was used, crashed at very end (sigh).
Fixed that crash behavior; no changes in outputs.
27 Aug 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 5 (MODIFY)
Well, usage+output shouldn't really change, but it should be more stable.
There is also a new opt: -align_centers_meth (read the help).
26 Aug 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 6 (ENHANCE)
much limiting of line lengths to 80 chars - should be no real change
25 Aug 2020, RC Reynolds, sqwave, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, siemens_vision, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use Dimon
25 Aug 2020, RC Reynolds, plug_3ddup.so, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, mritopgm, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, mayo_analyze, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use nifti_tool
25 Aug 2020, RC Reynolds, lpc_align.py, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use align_epi_anat.py
25 Aug 2020, RC Reynolds, ge_header, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use Dimon
25 Aug 2020, RC Reynolds, ftosh, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, ent16, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, check_dset_for_fs.py, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use afni_proc.py
25 Aug 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added new types TYPE_REMOVE and TYPE_REINSTATE
This is to track when programs or notable functionality gets removed.
25 Aug 2020, RC Reynolds, abut, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, Xphace, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, Ifile, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use Dimon
25 Aug 2020, RC Reynolds, FD2, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use afni
25 Aug 2020, RC Reynolds, DoPerRoi.py, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, Dimon1, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use Dimon
25 Aug 2020, RC Reynolds, AlphaSim, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dClustSim
25 Aug 2020, RC Reynolds, @snapshot_volreg3, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use @snapshot_volreg
25 Aug 2020, RC Reynolds, @make_stim_file, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use timing_tool.py
25 Aug 2020, RC Reynolds, @auto_align, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use align_epi_anat.py
25 Aug 2020, RC Reynolds, @UpdateAfni, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use @update.afni_binaries
25 Aug 2020, RC Reynolds, @DTI_studio_reposition, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dttest, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dttest++
25 Aug 2020, RC Reynolds, 3dproject, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dnoise, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dfim, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dDeconvolve
25 Aug 2020, RC Reynolds, 3ddup, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dbuc2fim, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dWavelets, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dUniformize, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dUnifize
25 Aug 2020, RC Reynolds, 3dProbTrackID, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dTrackID
25 Aug 2020, RC Reynolds, 3dMax, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dBrickStat
25 Aug 2020, RC Reynolds, 3dICC_REML.R, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dFourier, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dBandpass
25 Aug 2020, RC Reynolds, 3dFWHM, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dFWHMx
25 Aug 2020, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dDeconvolve
25 Aug 2020, RC Reynolds, 3dCountSpikes, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dToutcount
25 Aug 2020, RC Reynolds, 3dAnatNudge, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use align_epi_anat.py
25 Aug 2020, RC Reynolds, 3dAOV.R, level 2 (MINOR), type 7 (REMOVE)
removed from distribution
25 Aug 2020, RC Reynolds, 3dANALYZEtoAFNI, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 3dcopy or to3d
25 Aug 2020, RC Reynolds, 1dDW_Grad_o_Mat, level 2 (MINOR), type 7 (REMOVE)
removed from distribution - use 1dDW_Grad_o_Mat++
21 Aug 2020, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Fix header deps of underlying progs (namely, readglob.c).
Was crashing on some NIML reading cases.
09 Aug 2020, DR Glen, @ROI_decluster, level 2 (MINOR), type 1 (NEW_PROG)
Remove small clusters or single voxels in datasets with many ROIs
Keeps only the largest part(s) of the ROI with adjustable
threshold. Used for datasets with many ROIs, like those
found in an atlas. Can be used in combination with @ROI_modal_grow
03 Aug 2020, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fix sB update when changing surf order from 0,1 to 1,0
In only the case of setting the plugin surf_A/surf_B order to 1,0, the
need to update the surf_B index was not recognized, and it stayed at 1
(instead of the requested 0).
Thanks to D Glen for reporting the problem.
31 Jul 2020, P Taylor, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 1 (NEW_PROG)
Install MACAQUE_DEMO_REST_1.0, for macaque resting state FMRI examples.
Has a '-lite_version' opt for truncated EPI version, smaller download.
31 Jul 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior file path contained dots.
Joining filenames for output now fixed.
30 Jul 2020, P Taylor, @Install_MACAQUE_DEMO, level 3 (MAJOR), type 0 (GENERAL)
Now install MACAQUE_DEMO_2.1, which should be the new normal.
Script checks for things on install, makes recs, more full demo.
30 Jul 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Make easier to find template in case data has moved around.
Also use wildcard to clean intermed file, in case auto GZIP is on.
30 Jul 2020, DR Glen, vol2surf nzmode, level 2 (MINOR), type 2 (NEW_OPT)
nonzero mode option for 3dVol2surf and vol2surf plugin
Computes most common non-zero value along segment
30 Jul 2020, DR Glen, @ROI_modal_grow, level 2 (MINOR), type 1 (NEW_PROG)
Grow ROIs using nonzero mode in 1 voxel neighborhood increments
Similar functionality as in 3dROImaker but uses non-zero mode
to grow sets of regions, like those found in an atlas
28 Jul 2020, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
add initial afni_history_laurenpd.c
21 Jul 2020, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 6 (ENHANCE)
add env var control over pre-comp e2x, limit and pieces
See AFNI_MODEL_PRF_PRECOMPUTE_EX, AFNI_MODEL_PRF_MAX_EXP and
AFNI_MODEL_PRF_MAX_EXP_PIECES.
21 Jul 2020, RC Reynolds, get_afni_model_PRF_6, level 2 (MINOR), type 6 (ENHANCE)
add initial NT parameter
16 Jul 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update for shared libmri.so: linux_centos_7_64, linux_ubuntu_16_64
15 Jul 2020, P Taylor, 3ddot_beta, level 2 (MINOR), type 0 (GENERAL)
Moved header dep of suma_suma.h -> suma_objs.h.
Should be no output change.
15 Jul 2020, P Taylor, 3dVecRGB_to_HSL, level 2 (MINOR), type 4 (BUG_FIX)
Would whine when outputting BRIK/HEAD dset if -in_scal was used; fixed.
Also, moved dep of suma_suma.h -> suma_objs.h (shd be no output change).
15 Jul 2020, P Taylor, 3dTrackID, level 2 (MINOR), type 0 (GENERAL)
Moved header dep of suma_suma.h -> suma_objs.h.
Should be no output change.
15 Jul 2020, P Taylor, 3dTORTOISEtoHere, level 2 (MINOR), type 0 (GENERAL)
Moved header dep of suma_suma.h -> suma_objs.h.
Should be no output change.
15 Jul 2020, P Taylor, 3dNetCorr, level 2 (MINOR), type 0 (GENERAL)
Moved header dep of suma_suma.h -> suma_objs.h.
Should be no output change.
15 Jul 2020, P Taylor, 3dEigsToDT, level 2 (MINOR), type 0 (GENERAL)
Moved header dep of suma_suma.h -> suma_objs.h.
Should be no output change.
15 Jul 2020, P Taylor, 3dDTtoNoisyDWI, level 2 (MINOR), type 0 (GENERAL)
New opt for controlling random seed is available (for testing).
Also, moved dep of suma_suma.h -> suma_objs.h (shd be no output change).
01 Jul 2020, P Taylor, @Install_NMT, level 3 (MAJOR), type 1 (NEW_PROG)
Installer for the NIMH Macaque Template(s) v2, and the CHARM (atlases).
Courtesy of Ben Jung, Adam Messinger, et al.
23 Jun 2020, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE)
Add support for *.tsv and *.csv files
Tab and Comma separated value files will be read in, like 1D files, and
can be selected by a chooser, including in a plugin.
22 Jun 2020, P Taylor, convert_cdiflist_to_grads.py, level 2 (MINOR), type 4 (BUG_FIX)
Output col grads file was *not* scaled by bvalues, as help said it would.
Fixed: now output col grads multiplied by bvalues.
22 Jun 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 4 (BUG_FIX)
The -monty opt input was being ignored.
It now has a voice.
17 Jun 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 2 (NEW_OPT)
Add legend functionality, along with opts for label and loc specifying.
New opts: -legend_on, -legend_labels, -legend_locs.
14 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
For vstat with seedbased corr (rest), use 0.3 as thr value of corr map.
Returning value to what it had been for a long time, based on examples.
11 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Add Stride to graphing (every n-th time point, n=1..9)
10 Jun 2020, P Taylor, convert_cdiflist_to_grads.py, level 3 (MAJOR), type 1 (NEW_PROG)
For GE scanners, we might want a cdiflist* file for DWI grad info.
This prog converts such beasts into usable grad/bvalue files for proc.
09 Jun 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix behavior when -xticks_off and/or -yticks_off are/is used.
Now the specified axis will really be *empty*.
04 Jun 2020, P Taylor, fat_mat2d_plot.py, level 2 (MINOR), type 0 (GENERAL)
Improve couple things in help file; change def cbar.
More useful 'divergent' class of cbar as default.
03 Jun 2020, P Taylor, lib_mat2d_plot.py, level 3 (MAJOR), type 0 (GENERAL)
Many updates to functioning, defaults, reading argv, applying user opts.
Help file added as well; works with main proc: fat_mat2d_plot.py.
03 Jun 2020, P Taylor, fat_mat2d_plot.py, level 3 (MAJOR), type 1 (NEW_PROG)
FINALLY, a python3 program to plot 3dTrackID and 3dNetCorr output.
Plots *.grid and *.netcc files; replaces fat_mat_sel.py.
02 Jun 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Add PM (plus/minus) curve plotting options
Added to the 'Colors Etc' menu. Curves, Bars, and Fill.
01 Jun 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in populate_nifti_image(), call time series only if ntt>1 or NVALS==1
This is to avoid confusion when a time series is used to master a
non-time series dataset.
01 Jun 2020, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_regs and -show_regs_style
Show column indices or labels of an xmat.1D file with empty (all-zero)
regressors. An index list can be space or comma-separeated, or encoded.
Example 30 shows typical use cases.
Added for S Haller.
01 Jun 2020, P Taylor, lib_mat2d_base.py, level 2 (MINOR), type 0 (GENERAL)
Migrated from lib_mat2d.py; tweaks added.
Add in few more mat2d attributes; rearrange methods.
01 Jun 2020, P Taylor, lib_mat2d.py, level 2 (MINOR), type 0 (GENERAL)
Start some new functionality for 2D matrices.
In particular, these are for 3dTrackID and 3dNetCorr output.
01 Jun 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
For vstat with seedbased corr (rest), use 0.2 as thr value of corr map.
The value 0.3 seemed pretty high (esp. if no smoothing is applied).
01 Jun 2020, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL)
Add new funcs for convenient message printing, in the AFNI style.
IP(), EP() and WP(), which are wrappers to use APRINT().
01 Jun 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
Reformat report*.1D tables a bit.
Add in a KEY; change U/W to A/B; minor format stuff.
31 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Change range of grayscale when EPI is ulay (ve2a and LR flipcheck).
Now 2-98percent (nonzero).
31 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 4 (BUG_FIX)
Two bug fixes: 1) where src_prefix is defined.
2) Make sure labels/atlases of ATL|SEG followers are passed along.
30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 3 (MAJOR), type 1 (NEW_PROG)
Perform modal smoothing, and go back and add in any ROIs that were lost.
May be useful in @animal_warper; may be good to add mask stuff, too.
30 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL)
Default modal smoothing now is with replacement of any lost ROIs.
Uses @djunct_modal* script; opt to not replace. More QC images now, too.
30 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
String selector of lost ROIs now is only comma-separated list.
Discovered couldn't have both comma- and '..'-separated list in selector.
30 May 2020, P Taylor, @djunct_modal_smoothing_with_rep, level 2 (MINOR), type 0 (GENERAL)
Now use *.nii.gz files for all intermeds, not *.nii.
Works better with @animal_warper this way.
30 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Apply input_abbrev earlier in processing.
Homogenize naming, I think, if it is being selected.
28 May 2020, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Add curve smoothing plot to graph viewer
Invoked from 'Colors Etc' menu, or by pressing the 's' key. [For GC]
28 May 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Now report DF information in vstat block.
Needed to be able to interpret F-stat and t-stat values.
26 May 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Two major changes in output: ve2a and LR-flipcheck now have EPI as ulay.
Most anats are SSed, so better edges? Thanks for suggestion, O Esteban!
26 May 2020, P Taylor, @djunct_edgy_align_check, level 3 (MAJOR), type 0 (GENERAL)
Several changes to make this appropriate using EPI as ulay.
New opts, couple small bug fixes, couple tweaks.
26 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
Now output an AFNI-style string selector of 'lost' ROI values.
This might make it easier to see the diffs the volumes.
25 May 2020, RC Reynolds, Makefile.macos_10.12_local, level 2 (MINOR), type 6 (ENHANCE)
add libexpat.1.dylib to EXTRA_INSTALL_FILES
R was upgraded to 3.6 (on the 10.12 build machine), since that is the
current G Chen version requirement, making R_io.so work for people with
only 3.6. But libexpat was upgraded too, which afni depends on, meaning
systems needed that new version of libexpat, or afni would not work.
Instead, libexpat.1.dylib is now simply included with the binaries.
Thanks to S Gotts and K Tran for reporting the problem.
22 May 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL)
Change this prog to do all work in a workdir that can be cleaned.
Should not have any effect on the usage or outputs.
21 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT)
add options -NN1, -NN2 and -NN3
Also, fix tiny origin shift when large zero-padding is applied.
21 May 2020, P Taylor, afni_seeds_per_space.txt, level 3 (MAJOR), type 0 (GENERAL)
Keep up with change of macaque standard space naming: stereoNMT -> NMT2.
'stereoNMT' is an ex-parrot.
21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 3 (MAJOR), type 1 (NEW_PROG)
Adjunct program for @animal_warper.py; build ROI report table.
Thanks to D Glen and A Messinger for helpful feedback+inputs.
21 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL)
Add reports of warped and unwarped ROIs, via adjunct_aw_tableize*.py.
Thanks to D Glen and A Messinger for helpful feedback+inputs.
21 May 2020, P Taylor, adjunct_aw_tableize_roi_info.py, level 2 (MINOR), type 0 (GENERAL)
Require mode_smooth_size as input, and include it in table.
Thanks to D Glen and A Messinger for helpful feedback+inputs.
21 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Report now reports mode_smooth_size.
Thanks to D Glen and A Messinger for helpful feedback+inputs.
20 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update THD_mask_erode_sym() akin to take NN param
This matches the dglen update to THD_mask_dilate().
20 May 2020, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fix history and memory loss
19 May 2020, DR Glen, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
nzvolume - volume of nonzero voxels
18 May 2020, P Taylor, @animal_warper, level 3 (MAJOR), type 0 (GENERAL)
Large number of under-the-hood changes, as well as new opts.
More general handling of followers and choosing file abbrevs.
18 May 2020, P Taylor, afni_seeds_per_space.txt, level 2 (MINOR), type 0 (GENERAL)
Updated APQC seed locations for stereoNMT space.
More centralized now in GM and in specific ROIs; aud away from vessel.
14 May 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Large number of under-the-hood changes, for readability/clarity.
Change echo->printf, spacing, clear comments, etc. No output changes.
11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update web links to help pages in uber*.py
Update uber_align_test.py, uber_skel.py, uber_subj.py and uber_ttest.py.
11 May 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
updates for python3
Update xmat_tool.py, quick.alpha.vals.py, read_matlab_files.py,
uber_align_test.py and uber_skel.py.
04 May 2020, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 6 (ENHANCE)
make partual updates for python3
04 May 2020, RC Reynolds, suma-general, level 2 (MINOR), type 5 (MODIFY)
remove tabs from a bunch of files
04 May 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
fix download of test file
Thanks to Gerome on MB for reporting the problem.
04 May 2020, P Taylor, @Install_IBT_DATASETS, level 2 (MINOR), type 1 (NEW_PROG)
Installer for the Indian Brain Templates. Enjoy.
Courtesy of Dr. Bharath Holla, et al.
30 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 0 (GENERAL)
Added YouTube button to afni GUI.
29 Apr 2020, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY)
for recur, def to pub/dist/bin/misc; terminate on failed test download
29 Apr 2020, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 6 (ENHANCE)
add AFNI_DRIVE_OPTS_XVFB env var for adding opts to Xvfb
This will probably be modified later, but it allows one to pass
something like '-nolisten inet6' if IPv6 is not working.
Thanks to W-L Tseng.
27 Apr 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Added a help example for integrating output into afni_proc.py.
... because otherwise *I* forget how to use the outputs.
24 Apr 2020, P Taylor, 3dLMEr, level 2 (MINOR), type 0 (GENERAL)
Updating this R file for GC. So I don't really know what the changes do.
... though I reeeallly want to pretend the changes were mine, ALL MINE.
24 Apr 2020, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL)
Sidedness of testing will no longer be checked for non-stat thr vols.
It must be Daniel Glen's birthday today (two-sided, non-stat p<0.9999).
23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Added new help example.
Demonstrates useful colorbar-entry functionality.
23 Apr 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Use '-colorscale_idx_file ..' to control AFNI env var AFNI_COLORSCALE_xx.
Provides a way for user-created cbar info to be input+used.
21 Apr 2020, JK Rajendra, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added -all_dsets to load all datasets together.
14 Apr 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if dataset inputs had full paths, use them in proc script
Thanks to W-L Tseng for pointing out the discrepancy.
10 Apr 2020, RW Cox, AFNI gui, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm option for normal font sizes
08 Apr 2020, RW Cox, 1dplot, level 2 (MINOR), type 6 (ENHANCE)
Add '0' to the -dashed option
-dashed codes are now
1 = solid 2 = longer dashes
3 = shorter dashes 0 = no line, use boxes
Code 0 is new, to allow a graph with some data plotted
with lines and some without.
07 Apr 2020, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
add -see_also and -ver_man to help create a quick man page
To create a man page (via help2man), consider:
nifti_tool -see_also > nt.see_also.txt
help2man --help-option=-help --version-option=-ver_man \
--include nt.see_also.txt --no-info nifti_tool \
| gzip > nifti_tool_manpage.1.gz
after which one can install the file, or test via
man ./nifti_tool_manpage.1.gz
(see the uncompressed version for syntax).
31 Mar 2020, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 6 (ENHANCE)
update for python3
31 Mar 2020, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 4 (BUG_FIX)
fix lib_system_check:self.os_dist for newer python
30 Mar 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
have module_test_lib.py (and so afni_proc.py) work on python 2.6 again
Done for S Horovitz.
30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
rigid_equiv - rigid equivalent affine alignment
30 Mar 2020, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI view equivalent for epi2anat alignment fix
27 Mar 2020, DR Glen, @animal_warper center_shift, level 2 (MINOR), type 2 (NEW_OPT)
Allow for center shifting or not
24 Mar 2020, RC Reynolds, python_module_test.py, level 2 (MINOR), type 5 (MODIFY)
restore approximate previous behavior
23 Mar 2020, RC Reynolds, 3drefit, level 2 (MINOR), type 2 (NEW_OPT)
add options -oblique_recenter and -oblique_recenter_raw
Adjust the origin so the cardinalized 0,0,0 (e.g. seen in the afni GUI)
is in the same brain location as it was originally (in the scanner?).
So when viewing an oblique volume on top of a '3dWarp -deoblique' output,
coordinate 0,0,0 will match between them.
20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
fix PY_DIR, update PY vars, add list_py_libs
20 Mar 2020, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
fix PY_DIR, update PY vars, add list_py_libs
19 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix use of module_test_lib.py with change to new afnipy dir
17 Mar 2020, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT)
Modify font size options - hopefully easier now
1) Change meaning of 'plus' fonts to be bigger than before.
2) Change so that 'plus' twice on command line equals 'big'.
3) Add simpler options '-big' and '-plus' and '-minus'.
Combined, these should make it easier to do font size changes.
12 Mar 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
point web help for program to sphinx tree
Also, added -hweb/-h_web for python progs that use option_list.py.
12 Mar 2020, RC Reynolds, SUMA_test_DrawingAreaWidget, level 2 (MINOR), type 1 (NEW_PROG)
test for a valid DrawingAreaWidgetClass pointer
12 Mar 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL)
This program has been deemed unnecessary.
Thanks for the FS folks for discussions/clarifications on this.
12 Mar 2020, P Taylor, 3dReHo, level 2 (MINOR), type 0 (GENERAL)
Alter output format if ROI neighborhood values of ReHo are calc'ed.
Make 2 col (ROI val; ReHo val). Output multiple text files, if nec, too.
11 Mar 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Swap ulay/olay in va2t (anat->ulay); clearer image, maybe.
Make template (if used) ulay in most other QC blocks.
10 Mar 2020, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE)
Add dataset-level weights to 3dttest++
Per the request of users in Tulsa.
New options -setweight[AB] allow user to provide weights
for the importance of a user in the calculations.
05 Mar 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY)
for now, use mris_convert/3dcopy for extra annot files
So standard mesh version will not have a proper label table, but
the values will be appropriate and more usable in suma.
This is done to import the Schaefer/Yeo atlases onto standard meshes.
Done with D Glen.
27 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
add -fsannot_ver; apply -extra_annot_labels output as -extra_fs_dsets
27 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
New opt '-warpscale' added; is a new opt in 3dQwarp, can be tweaked here now.
Control flexibility of warps. Right now testing different values.
26 Feb 2020, RW Cox, machdep, level 2 (MINOR), type 6 (ENHANCE)
First step for allowing floating round randomization
Code in machdep.c, enabled by environment variable
AFNI_RANDOMIZE_ROUNDING, lets a program invoke macro RAND_ROUND to
randomize the IEEE rounding mode. This requires compiling with the flag
-DUSE_FENV to enable use of the C99 function fesetround() to set the
rounding mode -- see machdep.h. So far, only 3dAllineate has any parts
that use RAND_ROUND -- that is, if you set AFNI_RANDOMIZE_ROUNDING to
YES and run 3dAllineate, the results will change from a 'normal' run.
How much? That's the point of this update, to see how sensitive the
output is to the accumulation of tiny changes.
26 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Crashing in cases of 'pythonic' APQC with no censoring.
Have fixed now.
26 Feb 2020, DR Glen, @animal_warper ROIdset followers, modal smoothing, level 2 (MINOR), type 2 (NEW_OPT)
Allow for ROIs to follow into template space and modal smoothing
ROIs are transformed with nearest neighbor interpolation
Both ROIs and segmentation followers from the template space
are now modally smoothed within 3 voxel neighborhoods
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 0 (GENERAL)
New min|max range on vox size; update report text.
Based on tests with FS data.
25 Feb 2020, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fix, caught by RCR. Or was it first *added* by RCR????
... Nope. It was added by me. Sigh.
24 Feb 2020, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
Add -warpscale option
To scale the warp displacements down at each level, for experimentation.
22 Feb 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL)
Temporary files now have a random string in their prefix.
Thus, can have multiple runs in same directory simultaneously sans problem
.
22 Feb 2020, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Can control AGIF frame rate, using opt (-agif_delay) to control AFNI env var.
Thanks to RCR for pointing out the env var.
21 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Crashing in cases of 'basic' APQC with no outlier-based censoring.
Have fixed now.
19 Feb 2020, RC Reynolds, afni_python_wrapper.py, level 3 (MAJOR), type 1 (NEW_PROG)
replaces afni_util.py as a main
This program can theortically be used to call any AFNI python function
from the shell.
19 Feb 2020, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY)
no longer available as a main executable
19 Feb 2020, P Taylor, adjunct_select_str.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @djunct_select_str.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, adjunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @djunct_make_script_and_rst.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, adjunct_is_label.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @djunct_is_label.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, adjunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @djunct_combine_str.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, adjunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @djunct_calc_mont_dims.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, DoPerRoi.py, level 2 (MINOR), type 0 (GENERAL)
Renamed from @DoPerRoi.py.
Purge @ symbol in Python progs, for purpose of repackaging/distribution.
19 Feb 2020, P Taylor, @SSwarper, level 2 (MINOR), type 0 (GENERAL)
New QC image outputs added.
One for skullstripping (orig space) and one for warping (ref space).
18 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
help examples now include some developed outside of afni_proc.py
This includes some class demos, along with pamenc and NARPS.
Include a line about whether each example is reasonably recommended.
Done to appease the mighty P Taylor.
17 Feb 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Reorganized under the hood, deal with censoring in a better way.
Easier to tweak/update changes now.
17 Feb 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL)
Opt -censor_hline can now take a keyword NONE as an entry.
Useful if looking at multiple inputs and only some have censor lines.
14 Feb 2020, RW Cox, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Get Atlas Colors working again
Problem: 2 generations of overlay colorization changes.
a) Overlay went from indexes to RGB
b) Overlay went from indexes or RGB to RGBA
The atlas overlaying function didn't allow for these very well,
especially the latter. Obviously, this can't be my fault since I'm the
boss - even though I wrote the offending code. Someone must have joggled
my brain.
14 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -compare_opts_vs_opts
One can compare two afni_proc.py commands sequentially, that are
not part of the stored examples list. Consider:
afni_proc.py ... first option set ... \
-compare_opts_vs_opts \
... second option set ...
It is okay for 'second option set' to include the afni_proc.py
command name, in case two scripts are concatenated.
14 Feb 2020, DR Glen, @animal_warper dset followers, level 2 (MINOR), type 2 (NEW_OPT)
-dset_followers to apply same transformations as dset
14 Feb 2020, DR Glen, @Align_Centers shift xform, level 2 (MINOR), type 2 (NEW_OPT)
Move center/origin by known amount from 1D file
Large translations in nonlinear warp interpolation can use vast
amounts or memory in the 3dNwarpApply implementation. By doing
center alignment separately, we can remove the memory and
computational costs. The new options are -shift_xform and
-shift_xform_inv.
12 Feb 2020, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
add ability to compare against examples
Add options -compare_opts, -compare_example_pair, -show_example and
-show_example_names.
Consider these examples:
afni_proc.py -show_example 'Example 11b'
afni_proc.py -show_example_names
afni_proc.py ... my options here ... -compare_opts 'Example 11'
Motivated by C Gaillard and P Taylor.
12 Feb 2020, DR Glen, 3dCM Icent, Dcent, level 2 (MINOR), type 2 (NEW_OPT)
alternative centers
To force centers to lie within a region
-Icent for internal center, -Dcent for distance center
07 Feb 2020, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
reduce X11 program deps
Possibly define LLIBS_X11 in top-level Makefile (as current LLIBS) and
then remove X libs from LLIBS. M.INCLUDE will define LLIBS if not set.
Move suma_help to IMOBJS.
07 Feb 2020, RC Reynolds, Makefile.linux_fedora_28_shared, level 2 (MINOR), type 6 (ENHANCE)
build main non-X11, non-SUMA AFNI program without X deps
Set LLIBS_X11 to current LLIBS, and give it to SUMA_LINK_LIB.
Remove all X11 libs from LLIBS. Add -DREPLACE_XT to CEXTRA.
Note: without REPLACE_XT, LLIBS could still just use Xt and X11.
And made the same mods to Makefile.linux_xorg7_64.
05 Feb 2020, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -LJorder option
To order voxels by their Ljung-Box statistics.
05 Feb 2020, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
list all global options via 'PROG.py -optlist_show_global_opts'
Also, add -optlist_show_argv_array to display afni_proc.py options
in python dictionary format.
This could be done with any OptionList-based python program.
05 Feb 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add initial new library for processing example, lib_ap_examples.py
03 Feb 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
add -extra_annot_labels
03 Feb 2020, P Taylor, @djunct_anonymize, level 2 (MINOR), type 1 (NEW_PROG)
Anonymize files, and maybe add a note.
Can either edit input directly, or make a copy + edit that.
03 Feb 2020, P Taylor, @afni_refacer_run, level 2 (MINOR), type 2 (NEW_OPT)
Can anonymize output dsets: -anonymize_output.
Fairly self-explanatory opt.
02 Feb 2020, RW Cox, 3dPval, level 2 (MINOR), type 2 (NEW_OPT)
Add -qval option to 3dPVAL [for GC].
Merry Groundhog Day!
29 Jan 2020, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had RGB type, which happens for DEC maps.
Has been fixed now.
29 Jan 2020, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX)
The input opt '-xfile ..' was broken; now it is fixed.
Fix class inits, as well, under the hood.
27 Jan 2020, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
add basis=BASIS parameter when defining timing class
Done for geenaianni on MB.
27 Jan 2020, RC Reynolds, @diff.tree, level 2 (MINOR), type 2 (NEW_OPT)
add -show_list_comp, to do pairwise comparison of file names
27 Jan 2020, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 6 (ENHANCE)
gzip SUMA/*.nii, except for SurfVol
27 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL)
Program now outputs QC images automatically.
These are output into a PREFIX_QC directory each run.
27 Jan 2020, P Taylor, @SSwarper, level 3 (MAJOR), type 0 (GENERAL)
Large set of updates; many new opts added, too; generally much improved warps.
Heavily tested on 178 subj across studies; output fnames are same, though.
27 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in QC.
Broke when there was one stim used (bad scalar -> list conv).
26 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL)
This program now requires specifying a mode for re/defacing.
One can also output all types of re/defacing simultaneously.
24 Jan 2020, P Taylor, @afni_refacer_run, level 3 (MAJOR), type 0 (GENERAL)
This program has been revamped and updated, including having a new ref vol.
Syntax for running this has totally changed (options exist).
24 Jan 2020, P Taylor, @afni_refacer_make_master_addendum, level 3 (MAJOR), type 0 (GENERAL)
This program just records additional tweaks to refacer ref vol.
Not really meant to be run on its own; for future reference only.
23 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE)
add handling of magic version 4 (ROIs and mask==1 data)
Done for J Gonzalez-Castillo.
22 Jan 2020, RW Cox, 3dREMLfit, level 3 (MAJOR), type 6 (ENHANCE)
Compute Ljung-Box statistic for -Rvar dataset.
Provides a measure of how temporally correlated each voxel's
pre-whitened residuals are. Small LB value = good fit by the ARMA(1,1)
model. Sub-brick is coded as a chi-squared statistic for use in
thresholding in the AFNI GUI.
22 Jan 2020, RC Reynolds, plug_realtime, level 3 (MAJOR), type 0 (GENERAL)
add ROIs and data mask method
Added corresponding demo: AFNI_data6/realtime.demos/demo_3_ROIs_n_data
22 Jan 2020, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE)
add handling of magic version 3 (all data light)
21 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Increase thresholds and cbar range in vstat_seedcorr and regr_corr dsets.
Clearer QC, methinks, based on several different group dsets.
17 Jan 2020, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
New pieces of QC: corr brain image in regr block.
Shows corr of mean residual with everything. Have a nice day.
15 Jan 2020, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
corr_* dsets are now correlations with ROI averages
They were previously average correlations with each ROI voxel. The new
maps look similar, but are probably more natural and have nicer scales.
Requested by P Taylor.
14 Jan 2020, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Change text of animal_outs.txt.
Add in a couple new dsets to be listed.
13 Jan 2020, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
add some make lists ; see 'make list_lists'
13 Jan 2020, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
New pieces of QC: first, seedbased corr maps for non-task data.
Second, censor-based warnings (general and per-stim).
13 Jan 2020, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
New function to read in seed list text file.
Returns list of seed objs for APQC.
13 Jan 2020, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT)
Couple new options.
Can specify colorbar and center coords now.
31 Dec 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
Do not require out_limit. Currently will still show in driver.
Done for P Taylor.
27 Dec 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 2 (NEW_OPT)
New option(s) to not just *check* a dset for FS-ability, but to correct it.
The '-fix_all' and accompanying options control this. Bonne idee, DRG!
26 Dec 2019, P Taylor, check_dset_for_fs.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix one of the test criteria (-is_mat_even).
Thanks, S. Torrisi, for pointing this out.
25 Dec 2019, DR Glen, erosion/dilation neighborhoods, level 2 (MINOR), type 5 (MODIFY)
Allow for NN1,NN2,NN3 neighborhoods for erosion and dilation
3dAutomask and other programs use these functions
the depth option in 3dAutomask gives a depth of automask NN1,2,3
17 Dec 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
allow labels as column selectors when reading xmat.1D files
Done for G Chen.
12 Dec 2019, RW Cox, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Add -zcensor option
Remove from consideration any time point t where xset(t) OR yset(t) is
identically zero (in the mask). For Peter Molfese and Emily Finn.
Merry X!
12 Dec 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY)
More centers - find deepest near voxel closest to Center of Mass
Came from CodeConvergence idea by Meghan Robinson
Voxel closest to center of mass is similar to latest ICent
in Clusterize GUI
10 Dec 2019, RW Cox, AFNI GUI, level 2 (MINOR), type 3 (NEW_ENV)
Add 'Zoom lock' to the locking capability
Also a new environment variable AFNI_ZOOM_LOCK to turn this on at
startup, vs interactively later.
10 Dec 2019, RC Reynolds, uber_proc.py, level 2 (MINOR), type 5 (MODIFY)
separate into main/lib/gui, so one can run -help w/out PyQt4
09 Dec 2019, RC Reynolds, 3dTagalign, level 2 (MINOR), type 2 (NEW_OPT)
add -tagset
Coded by T Holroyd.
29 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -volreg_opts_ewarp, to pass additional volreg EPI warp options
Added for L Fernandino.
26 Nov 2019, RW Cox, @afni_refacer_run, level 3 (MAJOR), type 6 (ENHANCE)
Modify shell dataset to avoid some brain clipping
Mostly by eroding the inside of the brain shell.
Also a couple little tweaks to the script.
21 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
update babble about FreeSurfer in help
21 Nov 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 4 (BUG_FIX)
add 'endif' for if( $warpdrive_method == '3dWarpDrive'
Thanks to T Holroyd for reporting and fixing this.
21 Nov 2019, RC Reynolds, 3dRank, level 2 (MINOR), type 4 (BUG_FIX)
fix storage_mode handling (re-allow niml.dset output)
Thanks to dmoracze on the Message Board for noting the problem.
19 Nov 2019, RC Reynolds, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
add -fs_setup, to optionally source $FREESURFER_HOME/SetUpFreeSurfer.csh
14 Nov 2019, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 0 (GENERAL)
New output: fs_ap* dsets for tissue-based reg in afni_proc.py;.
New output: *REN_gmrois* dsets for tracking/corr mats in FATCAT.
14 Nov 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-make_rank_dsets ..', bc *rank* dsets no longer make by def.
The *REN* dsets should be used instead; opt just for back compatibility.
13 Nov 2019, DR Glen, AFNI Clusterize, level 2 (MINOR), type 4 (BUG_FIX)
ICent error
Couple bugs in ICent location computation - thx to Meghan Robinson
12 Nov 2019, DR Glen, @measure_erosion_thick, level 2 (MINOR), type 5 (MODIFY)
Center for deepest voxel closest to Center of Mass
Made in CodeConvergence with Chris Rorden and Meghan Robinson
11 Nov 2019, DR Glen, @suma_acknowledge, level 2 (MINOR), type 1 (NEW_PROG)
Make simple graphs of collaborations and classes
Made for AFNI bootcamps using SUMA graph datasets
This may be useful for acknowledgement for general use
01 Nov 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
process out.mask_at_corr.txt, the anat/template Dice coefficient
Requested by P Hamilton.
01 Nov 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
create out.mask_at_corr.txt, the anat/template Dice coefficient
Requested by P Hamilton.
25 Oct 2019, RW Cox, afni GUI driver, level 2 (MINOR), type 6 (ENHANCE)
butpress commands to image viewer
butpress=Colr or Swap or Norm to simulate button presses
For Paul.
25 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow selectors on -dset* options (cannot mix with removal options)
Requested by E Finn.
24 Oct 2019, RW Cox, AFNI gui, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_IMAGE_COLORSCALE defines colorbar for image viewer window
Formerly fixed, now user can specify the color scale to use here from
one of these: magma viridis plasma googleturbo
Also, I restored the 'g' (gamma) button affect on this color scale.
24 Oct 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add combine methods m_tedana, m_tedana_OC
Can run tedana from MEICA group:
https://github.com/ME-ICA/tedana
https://tedana.readthedocs.io
23 Oct 2019, P Taylor, check_dset_for_fs.py, level 3 (MAJOR), type 1 (NEW_PROG)
Script to check properties of a dset, see if suitable for FS's recon-all.
The check criteria have been built over time, empirically.
16 Oct 2019, RC Reynolds, @auto_tlrc, level 2 (MINOR), type 6 (ENHANCE)
re-insert updates from 2019.05.29, plus updates for -init_xform
15 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
add -subbrick_info, to write only 'At sub-brick #N' info to stdout
11 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
checked and merged another 17 commit PR from pn2200
This is mostly to resolve missing prototypes.
10 Oct 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
add -niml_hdr, to write full NIML header(s) to stdout
09 Oct 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
checked and merged 30 commit PR from pn2200
This is mostly to resolve compiler warnings.
07 Oct 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
probably the last set of test updates for now
07 Oct 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Change text of animal_outs.txt.
Minor 'under the hood' changes, too.
03 Oct 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 0 (GENERAL)
Just divvied up the behavior of the functions better.
Also have a general, NxN case .
02 Oct 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL)
The naming convention of PE dist dir has been reversed; mask opts changed.
PE dist dir should match with JSONs better; 3dmask_tool does masking now.
02 Oct 2019, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 0 (GENERAL)
Output more specific information about finding unexpected negative values.
Tell user the [row, col] of potentially bad values, for easier QC.
30 Sep 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
added test scripts under commands, along with cmake versions for build
13 Sep 2019, P Taylor, 3dWarp, level 2 (MINOR), type 2 (NEW_OPT)
New opt: -disp_obl_xform_only.
Better way to get transform between obl coords than cat_matvec trickery.
12 Sep 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL)
Output QC directory of images now, as well. Useful for quick QC.
Later, will add some checks for obl, to not smooth unnec.
10 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Unifize output in standard space.
Better for visualization in afni_proc.py QC.
06 Sep 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Two minor changes: montages now separated by 1 gap line.
... and show censor bars in VR6 plots, if censoring.
06 Sep 2019, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL)
Now use montgap=1 by default.
This is for APQC applications, where subj data fills FOV.
06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Output skullstripped version of template in std space.
Also add 'notes' to that file, so gen_ss*script* can find template.
06 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
Put QC images into subdir called QC; output mask.
Few other tiny changes/reorganizations internally.
04 Sep 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opts: -obl_resam_ulay OIU, -obl_resam_Olay OIO, -obl_resam_box OIB.
Control resampling of dsets (ulay, olay, focus box) when applying obl.
04 Sep 2019, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-extra_fs_dsets ..', to translate more FS-created surf/ dsets.
Allow more FS surf dsets to be brought into SUMA. For F. Lalonde.
03 Sep 2019, P Taylor, @animal_warper, level 2 (MINOR), type 0 (GENERAL)
New QC imaging with @chauffeur_afni; mask created, too.
And a few minor changes under the hood, worked out with DRG.
30 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix input opt to change blur size; was broken before, crashing prog.
Thanks, L. Dowdle for finding!
30 Aug 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opts: -edge_enhance_ulay EE, -obliquify OBL.
Different way to enhance edges of ulay, and apply obliquity info.
30 Aug 2019, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
supersize
supersize - larger range of scaling for smaller animals to template
30 Aug 2019, DR Glen, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT)
more options+fixes
AFNI view reset for NIFTI
feature_size and supersize options for smaller animals
29 Aug 2019, P Taylor, @auto_tlrc, level 3 (MAJOR), type 0 (GENERAL)
RE-introducing the program '@auto_tlrc' to the distribution.
It had been mistakenly deleted somehow.
29 Aug 2019, DR Glen, @animal_warper, level 2 (MINOR), type 2 (NEW_OPT)
slew of options
ok_to_exist for restarts, template and segmentation output
prefixes, rigid/rigid_equiv/affine/all alignment,
follower data
28 Aug 2019, P Taylor, lib_gershgorin.py, level 2 (MINOR), type 1 (NEW_PROG)
Funcs to answer question: is this aff12 matrix very different from I?
Uses fun algebraic facts known to and shared by the inimitable RWC.
28 Aug 2019, P Taylor, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
Matrix-y things: read_aff12_to_mat34(), matrix_multiply_2D().
And supplements: matrix_sum_abs_val_ele_row(), calc_zero_dtype().
27 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 0 (GENERAL)
Added more fields to the output param text file.
Also added to the help file (including *about* the params text file).
27 Aug 2019, P Taylor, 3dSpaceTimeCorr, level 2 (MINOR), type 2 (NEW_OPT)
New opts: '-freeze* ..' that allow one to fix a location in dset A.
Input for Zhihao Li.
26 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
linux_fedora_28_shared: make libSUMA.so as a shared object
2.4 GB binaries -> (libmri.so) 600 MB -> (libSUMA.so) 200 MB
23 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed calculation when PE effective echo spacing is input.
The conversion to BWPP was wrong; led to almost no distortion corr.
23 Aug 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt, '-edgy_ulay': can turn ulay into edge-ified version of itself.
Useful for showing alignments.
22 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
(w/dglen) thd_gifti: remove INDEX_LIST DA from from list
When converting a GIFTI dataset to NIML, any index list should be
separated early, so as not to affect the SPARSE_DATA NIML element.
Thanks to T Holroyd for noting the problem.
19 Aug 2019, RC Reynolds, 3dDeconvolve_f, level 2 (MINOR), type 4 (BUG_FIX)
matrix_f.[ch]: dupe matrix_augment_01_columns from matrix.[ch]
When choosing between more local functions and those included in a
linked library, some systems seem to go all-or-nothing for one file
at a time. So for 3dDeconvolve_f, matrix_f.c needs everything that
might come from matrix.c. Otherwise we should have matrix_f.h rename
all of those functions, to avoid relying on compiler choices.
15 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
build R_io.so with usable link to libmri.so
Modify Makefile.linux_fedora_28_shared and Makefile.INCLUDE to control
creation of Makevars via R_IO_MODIFY_LINUX.
15 Aug 2019, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL)
add other_builds/OS_notes.linux_fedora_30.txt
Works with Makefile.linux_fedora_28_shared.
15 Aug 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 0 (GENERAL)
This program has been pretty fully revamped, and might be worth using now.
New scaling from Vinai, several updates/fixes/changes from last ver.
15 Aug 2019, DR Glen, @animal_warper, level 3 (MAJOR), type 1 (NEW_PROG)
Warp data to template and atlas segmentation to subject
Tested for macaques.
Derived from macaque_align.csh and NMT_subject_align.csh
14 Aug 2019, DR Glen, @FindAfniDsetPath append_file, level 2 (MINOR), type 2 (NEW_OPT)
Append file name to path with -append_file option
Useful for atlas names to full dataset names and other scripting purposes
13 Aug 2019, DR Glen, whereami atlas dataset, level 2 (MINOR), type 2 (NEW_OPT)
return dataset given atlas name(s)
Print atlas dataset for each input atlas
whereami -atlas TT_Daemon -show_atlas_dset prints TTatlas+tlrc
each -atlas atlasname prints the corresponding atlas dataset
13 Aug 2019, DR Glen, @FindAfniDsetPath atlas name search, level 2 (MINOR), type 5 (MODIFY)
Search SUPP_ATLAS_DIR path and look for atlases by name
Search additional directory for extra atlases and by name
Can search for TT_Daemon (atlas name) or TTatlas+tlrc (atlas dataset)
08 Aug 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
be more merciful in the case of timing overlap
- ISI stats: allow and adjust for stim overlap
- dur stats: show file/condition with stats
- match output between python2 and python3
07 Aug 2019, RC Reynolds, rPkgsInstall, level 2 (MINOR), type 6 (ENHANCE)
more programs that need R_LD_LIBRARY_PATH
Full list: 1dRplot, 3dICC, 3dISC, 3dLME, 3dMEMA, 3dMEPFM, 3dMVM, 3dPFM,
3dRprogDemo, 3dSignatures, ExamineXmat, MBA, RBA, rPkgsInstall.
05 Aug 2019, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
check for matplotlib.pyplot
05 Aug 2019, RC Reynolds, 3dMVM, level 2 (MINOR), type 5 (MODIFY)
set R_LD_LIBRARY_PATH for all 3d* R-calling programs using $afpath on osx
For macs: to allow R_io.so to load shared libraries needed by libmri,
set the search path to include the abin, flat_namespace and
R lib dir.
This might apply to linux with libmri.so, as well.
Thanks to N Adleman, C Caballero and E Silson.
01 Aug 2019, P Taylor, epi_b0_correct.py, level 2 (MINOR), type 0 (GENERAL)
Rename internal vars and opt names.
Improving internal notation-- still very much a beta program version.
27 Jul 2019, P Taylor, 3dDWUncert, level 2 (MINOR), type 0 (GENERAL)
Insert a couple ifdefs around OMP functionality.
This should allow program to compile even without OpenMP.
26 Jul 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -make_backup and -echo
Suggested by J Rajendra.
25 Jul 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -volreg_warp_master, for controlling the output grid
Added for Y Miyawaki.
25 Jul 2019, P Taylor, epi_b0_correct.py, level 3 (MAJOR), type 1 (NEW_PROG)
Program to apply freq volume to EPI for B0 distortion correction.
An honor to translate this program from one by Vinai Roopchansingh!
24 Jul 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_tsv_label_details option
22 Jul 2019, DR Glen, @Install_D99_macaque,NIH_Marmoset, level 2 (MINOR), type 4 (BUG_FIX)
download script bugs
tar platform differences and filename updates
19 Jul 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 6 (ENHANCE)
add use of HDR/NIM_SLICE_TIMING_FIELDS for -field option
This allows -{disp,diff}_{hdr,nim} an easy specification of
fields related to slice timing.
18 Jul 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for multi-echo data in find_tcat
18 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Hadn't merged in updated library functions, so apqc_make_tcsh.py crashed.
Updated library file in distribution now.
17 Jul 2019, RW Cox, AFNI gui, level 2 (MINOR), type 6 (ENHANCE)
changes to make alpha and boxed (A and B) work with color panes
People from Wisconsin are trouble.
17 Jul 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
another fix for 32-64 bit NIFTI update for older xorg7 systems
In thd_niftiread.c, cast nim->nz as int for EDIT_dset_items().
Newer C libraries seem to handle the possibility of 8 bits better,
but we are reading as 4. Thanks again to R Birn.
16 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Fix incompatibility with py2.
Sigh.
15 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Add in obliquity values in vorig QC block.
Also simplify text of radcorr block (fewer lines, less unnec repetition).
10 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL)
Can have text in the image tables now.
Facilitates labelling, commenting, etc.
09 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL)
Allow for multiple scripts to be executed, run and combined into 1 page.
Single script tarball, single RST, can have multiple scripts/reflinks.
08 Jul 2019, P Taylor, @djunct_make_script_and_rst.py, level 2 (MINOR), type 0 (GENERAL)
Allow wildcard chars in IMAGE descrip; SUBSECTIONS added.
Minor tweaks for formatting help files.
05 Jul 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
(useless) switch to 3dTcorr1D for dot product
Drops 2 commands down to 1 for computing corr_* volumes.
03 Jul 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Expanded vstat QC block capabilities.
Other tweaks, QC block IDs now in titles.
01 Jul 2019, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Labels on stim regressors, vorig QC block added, grayplot pbvorder/enorm.
Help updated; output stats still if not align/tlrc blocks used.
01 Jul 2019, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL)
Some minor tweaks to APQC HTML: better pbar size control, spacing.
Also can interpret pbar text more broadly.
28 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
add vr_base_dset uvar
27 Jun 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -write_with_header and -write_xstim
26 Jun 2019, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
New opt '-weight_ts WTS' to multiply ROI ave time series.
Input at the behest of Colm C. May it pour forth wondrous results.
25 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
get TSNR on surface
25 Jun 2019, P Taylor, 3dSkullStrip, level 3 (MAJOR), type 5 (MODIFY)
Dset orient should no longer affect results (b/c of var of init cond).
Intermediate resampling now reduces/removes var due to start.
19 Jun 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
add surf_vol uvar
14 Jun 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
add Makefile.linux_fedora_28_shared, to distribute a shared lib package
This uses libmri.so, though other libraries should be added (SUMA).
R programs do not yet work, as linking for R_io.so needs to be fixed.
14 Jun 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -hostname and -distdir
This is to allow places to mirror some of the AFNI site.
12 Jun 2019, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
better prep for shared build, and fix shared build of suma_gts_progs
Move mri_render.o out of libmri (corresponds with plug_render.so).Still ne
ed to fix mpeg_encode.
04 Jun 2019, RC Reynolds, plug_tag, level 2 (MINOR), type 4 (BUG_FIX)
use calloc to init last 4 bytes of tag string in thd_dsetatr.c
This was leaving garbage in HEAD file.
Thanks to A Nugent for noting the problem.
04 Jun 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
add -dset_extension, -storage_mode
03 Jun 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow ricor processing in case of multi-echo data
Done for K Dembny.
30 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 5 (MODIFY)
apply full Gaussian for blur, rather than truncated
Truncated is okay, but has cubical extents, rather than spherical.
29 May 2019, DR Glen, @auto_tlrc, level 2 (MINOR), type 5 (MODIFY)
auto_tlrc changes
NIFTI in and out fixes, prefix option, 3dAllineate option
Default interpolation changes, one pass combination default too
24 May 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
4+1 new features
1) Default threshold is now 0
2) Default threshold scale is now 0-10 instead of 0-1
3) Default max threshold scale exponent is now 5 instead of 4
4) Default colorscale is now Reds_and_Blues_Inv
PLUS
5) User can set AFNI_AUTORANGE_PERC to have the autoRange computed as
percentile point (from 2-99) of the nonzero absolute values in the OLay
brick. However, this doesn't work with warp-on-demand datasets now, so
it is confusing. Therefore, the default setting of this is 0, which
leaves the autoRange to be the maximum absolute value.
23 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -regress_anaticor_full_gaussian, -regress_anaticor_term_frac
Also, save fanaticor_mask_coverage dataset.
23 May 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Would not run in python2, because of subprocess.run() call (only py3).
Now updated to using afni_base.py functions to execute shell cmds.
22 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
blurs are now truncated Gaussians by default, making them flat
22 May 2019, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Somewhat big changes: warns block updated and radcor block added.
Left-right flip and @radial_correlate checks now in; other tweaks.
22 May 2019, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL)
Improved help file (lists blocks, line to online help).
Better formatting of a couple things; warn level coloring added.
22 May 2019, P Taylor, @djunct_json_value.py, level 2 (MINOR), type 1 (NEW_PROG)
Tiny program to extract values from JSONs.
Just used by apqc_make_tcsh.py.
20 May 2019, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
modify pane_scale to match updates for AFNI_PBAR_FULLRANGE
16 May 2019, RC Reynolds, gen_ss_review_scripts, level 2 (MINOR), type 6 (ENHANCE)
add uvars flip_check_dset and flip_guess
Add 'flip guess' to review_basic output.
16 May 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add read_text_dictionary, read_text_dict_list, convert_table2dict
Also, allow table2dict in write_data_as_json. This allows for easy I/O
of tables, and the ability to convert them to json form.
15 May 2019, RC Reynolds, gen_ss_review_scripts, level 2 (MINOR), type 6 (ENHANCE)
add uvar have_radcor_dirs
15 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 6 (ENHANCE)
modify output file names to handle special cases of all_runs and errts
14 May 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -radial_correlate_blocks and -radial_correlate_opts
Run @raidal_correlate at the end of each specified block, creating one
correlation volume per run. Each voxel gets the correlation of its time
series with a local (slightly Gaussian weighted) average.
14 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 0 (GENERAL)
Change some fields in pbar json, for greater utility.
Also make new default ftype for output cbar (jpg).
14 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
More pbar control: put in afni's '-XXXnpane P' behavior.
Same option name used in this prog.
13 May 2019, DR Glen, 3dExchange, level 2 (MINOR), type 1 (NEW_PROG)
Exchange specified values in a dataset
Takes two columns of numbers to map input to output
10 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Allow for comments about pbar ranges to be stored when saving pbar.
Also, the pbar text info will now be stored in dict/JSON-able form.
09 May 2019, RC Reynolds, @radial_correlate, level 2 (MINOR), type 2 (NEW_OPT)
replace 3dLocalstat with 3dmerge for locally ~averaged time series
One can choose between the methods, but 3dmerge is much faster.
Included options are -use_3dmerge, -corr_mask and -merge_nrad,
as well as -do_clean and -verb.
08 May 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
allow AFNI_BLUR_FIRFAC to get near zero
This can be abused for a 'fast ANATICOR', for example.
Since sigma = 0.4246609 * fwhm, consider using:
sfac = 1/(2*.0.4246609) = 1.17741
That number of sigmas should match the half width at half max,
which should terminate the blur just after a half height.
Or use 2*FWHM and sfac = 1.17741/2 = 0.588705 to make it more flat,
with a min contribution of ~0.84, rather than 0.5, yet limiting
the output to the same HWHM radius (e.g. FWHM=80mm with sfac=0.589
results in a fairly flat blur out to a radius of ~20 mm).
07 May 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -timing_to_1D_warn_ok to make some conversion issues non-fatal
Done for J Wiggins and M Liuzzi.
07 May 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
add deg2chordlen() to return distance traveled due to a rotation
01 May 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Allow -set_subbricks to take string labels for subbricks as usable args.
Excellent idea, Rasmus!
29 Apr 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Keystrokes for cluster jumpingn jumps to the next cluster's peak/cmass
N jumps to the previous cluster's peak/cmass
If focus is NOT in a cluster, then goes to the nearest
cluster in space instead. [For John Butman, NIH/CC - happy NOW?]
25 Apr 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
-regress_bandpass now takes any positive number of frequencies pairs
Done to appease the mighty P Taylor.
22 Apr 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -tsv_labels
This can be used to specify column labels to be used for
onset time, duration, trial type, and optional modulators.
19 Apr 2019, P Taylor, @Spharm.examples, level 2 (MINOR), type 0 (GENERAL)
Just updated paths/names: tarball getting used no longer exists.
No change in functionality (j'espere).
18 Apr 2019, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT)
Include -deoblique and -giant_move opts.
For oblique data, and/or heavily rotated, shifted, etc.
16 Apr 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
verify av_space == +tlrc before setting template
Thanks to P Molfese and P Taylor for noting the problem.
16 Apr 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
if do_apearch, update .bashrc to source all_progs.COMP.bash
Done to appease the mighty P Taylor.
15 Apr 2019, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Make -bysub option work with directory names
A command like
afni -bysub ~/data/UCLA_pamenc20
will find all 'sub-*' subdirectories in the given directory, and process
those individually via the older '-bysub' operation. This makes it
simple to read in an entire BIDS hierarchy. Note that the recursive
descent for each 'sub-XXX' name will include derivatives (if found).
12 Apr 2019, DR Glen, unWarpEPI.py python3, level 2 (MINOR), type 5 (MODIFY)
unWarpEPI.py python3 compatible
12 Apr 2019, DR Glen, unWarpEPI.py python3, level 2 (MINOR), type 5 (MODIFY)
unWarpEPI.py python3 compatible
11 Apr 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add functions gaussian_at_fwhm, gaussian_at_hwhm_frac
11 Apr 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -combine_tedort_reject_midk
It might be a good idea to set this to 'no', so less gets rejected.
11 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Brainnetome atlas
This atlas is now included in the standard distribution
This also is in the default list of atlases
08 Apr 2019, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 2 (NEW_OPT)
add options -reject_midk and -reject_ignored
It seems likely that '-reject_midk 0' should be the default.
07 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Eickhoff-Zilles 2.2 MPM atlas
This atlas is the newer 2.2 version of the MPM atlas
This atlas replaced the 1.8 version in the list, but both
are kept in the binary distribution
05 Apr 2019, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
HCP Glasser atlas in AFNI atlases
Mike Beauchamp and Meghan Robinson contributed atlas
Now included and first in default list too
This atlas is in MNI space (not in its original Contee
grayordinate surface space.
Additionally, all the pmaps (probability maps) have been
removed from the standard distribution and default list
20 Mar 2019, RC Reynolds, dcm2niix_afni, level 2 (MINOR), type 4 (BUG_FIX)
sync crorden/dcm2niix_console with repo, version v1.0.20181125
This is possibly to correct a bug with -m and partial brain coverage.
15 Mar 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
include tr field in uvars, and report it as TR in basic
15 Mar 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Better behavioring of -box_focux_slices when ulay and refbox grids differ.
Now checking grid similarity and resampling refbox if needbe.
14 Mar 2019, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
add gifti/regress_tests tree
This was also added to https://github.com/NIFTI-Imaging/gifti_clib repo.
10 Mar 2019, RW Cox, 3dXClustSim (ETAC), level 2 (MINOR), type 0 (GENERAL)
Sort FOM results to cast out duplicates from same iteration
Should make Global ETAC slightly less conservative.
08 Mar 2019, RW Cox, InstaCorr, level 2 (MINOR), type 4 (BUG_FIX)
Bandpass error found by the wandering Spaniard
Problem: very long time series (over 2000) analyzed *without* Bandpass
would give error message and then give useless results.
Solution: if Bandpass is turned off, that is signaled by setting the
upper freq cutoff to a large value. Then the FFT cutoff index is
computed from that as jtop = ftop/df where df = 1/N*dt, so we have
jtop = ftop*N/dt. For large N and large ftop, this is integer overflow.
Therefore, compute jtop in float, not int, then check it first. D'oh.
07 Mar 2019, RC Reynolds, gen_ss_review_table.py, level 3 (MAJOR), type 2 (NEW_OPT)
add -report_outliers and support options
Add -report_outliers_{fill,header}_style, -write_outlier, and
-outlier_sep for controlling the table presentation.
Will use -write_table instead of -tablefile going forward.
06 Mar 2019, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
if VR mismatch warning, specify whether AFNI uses the field
Done for B Benson.
05 Mar 2019, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
show subject counts; change line len and ddirs; no require on restricted
28 Feb 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
mask dset must include extension
27 Feb 2019, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Include grayplots in the APQC HTML file.
Should add some extra info about residuals/modeling/the meaning of life.
27 Feb 2019, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL)
Put a try/except at start, to set MPLBACKEND env if running w/o DISPLAY.
Useful for current settings on Biowulf (and possibly elsewhere).
26 Feb 2019, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
add -dset_sid_list, -hpad, -tpad
Add -dset_sid_list to specify subject IDs explicitly.
Also, add -hpad/-tpad; less indentation for 3dttest++.
25 Feb 2019, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
add modulators to -multi_timing_to_event_list output
Done for D Jangraw.
25 Feb 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
try to get mask_dset from TSNR output
22 Feb 2019, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
handle shells with paths in get_current/login_shell()
22 Feb 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -tlrc_NL_force_view, to handle sform_code=2 in auto_warp.py result
Done for I Berteletti.
19 Feb 2019, P Taylor, apqc_make_tcsh.py, level 5 (SUPERDUPER), type 0 (GENERAL)
Much functionality changed/improved (hopefully).
More output, better formats, help and HTML framework.
19 Feb 2019, P Taylor, apqc_make_html.py, level 5 (SUPERDUPER), type 0 (GENERAL)
Much functionality changed/improved (hopefully).
More output, better formats, help and HTML framework.
19 Feb 2019, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL)
Line thickness of plots now adjusts with number of points.
Useful as the number of time points increases (hopefully).
11 Feb 2019, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
... and can also turn off initial skullstripping and/or anisosmoothing.
Options cleverly named: -skullstrip_off and -aniso_off.
11 Feb 2019, P Taylor, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
Can turn off initial unifizing with -unifize_off.
Useful if unifizing has been done to dset before using this cmd.
07 Feb 2019, RC Reynolds, demoExpt.py, level 2 (MINOR), type 1 (NEW_PROG)
will now actually distribute Vinai's demoExpt.py and afniInterfaceRT
05 Feb 2019, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
-infile_list now implies -no_wait
05 Feb 2019, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX)
allow -extent to vary across datasets
05 Feb 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Had been missing an endif.
Now new and improved-- with endif!
30 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -volreg_post_vr_allin and -volreg_pvra_base_index
These are to run 3dvolreg (or 3dAllineate) to a base within
each run, before concatenating a transformation from each
per-run base to the global EPI registration base.
30 Jan 2019, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 2 (NEW_OPT)
Added '-montgap' and '-montcolor', for montage functionality.
Users can now control montage borders (i.e., gaps) and color.
30 Jan 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Added '-montgap' and '-montcolor', for montage functionality.
Users can now control montage borders (i.e., gaps) and color.
28 Jan 2019, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
updates to make target, prog_list
- grep out CMakeLists.txt
- add some ptaylor python scripts
- define and add DISCO_SCRIPTS
28 Jan 2019, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
add -help to @djunct_*.py
28 Jan 2019, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Well, new functionality to existing opt: make focus box from ulay or olay.
Keywords AMASK_FOCUS{O,U}LAY can be given to -box_focus_slices.
25 Jan 2019, P Taylor, @djunct_slice_space, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had subbrick selectors from @chauffeur*.
Has been fixed now.
25 Jan 2019, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Couldn't deal with volumes that had subbrick selectors from @chauffeur*.
Has been fixed now.
22 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_est_blur_detrend
We might change the default to no detrending here.
22 Jan 2019, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -show_obsoletes[_grep] and -show_system_progs
Inspired by Z Saad.
19 Jan 2019, P Taylor, @SSwarper, level 2 (MINOR), type 4 (BUG_FIX)
Program wouldn't run with '-odir ..' opt.
Now it will.
18 Jan 2019, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
process df_info, and hand off new uvars
18 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
run 1d_tool.py -show_df_info, unless -regress_show_df_info no
17 Jan 2019, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -show_df_info, to partition degrees of freedom in X-matrix
16 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
-regress_mot_as_ort now defaults to yes; use vr_base_external
This should not affect results, it is prep for other evil designs.
08 Jan 2019, RW Cox, @SSwarper, level 2 (MINOR), type 2 (NEW_OPT)
Add '-nolite' option
For backwards compatibility and testing.
08 Jan 2019, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY)
-lite is now the default -- for speed
Based on using @SSwarper with and without -nolite on 31 datasets.
Results are very similar, and no systematic differences between
the -lite and -nolite groups observed in mean or stdev.
08 Jan 2019, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -volreg_method, and corresponding options
This allows one to use 3dAllineate for EPI motion registration.
Options -volreg_allin_cost and -volreg_allin_auto_stuff (as well as
the old -volreg_opts_vr) can be used to control -cost and other options.
04 Jan 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 5 (MODIFY)
add -mod_hdr2, specific to NIFTI-2 headers
04 Jan 2019, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
add regression testing scripts
03 Jan 2019, RW Cox, @afni_refacer_XXX, level 2 (MINOR), type 1 (NEW_PROG)
Scripts to re-face a T1-weighted dataset
@afni_refacer_make_master = makes the 'shell' dataset used to replace
the face
@afni_refacer_run = runs re-facing on one input dataset
03 Jan 2019, RC Reynolds, nifti_tool, level 2 (MINOR), type 5 (MODIFY)
have -mod_hdr/-swap_as_nifti fail on valid NIFTI-2 header
Re-allow processing of ASCII headers (via NIFTI-2).
Also, incorporate updates from H Johnson.
26 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
incorporate more updates from the NIFTI_Imaging/nifti_clib repo
21 Dec 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 4 (BUG_FIX)
Adjusted coordinator for a couple situations.
Should be more centered for both 3D and 4D applications.
20 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
incorporate updates from the NIFTI_Imaging/nifti_clib repo
And update Makefile.INCLUDE.
19 Dec 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
show execution syntax in both tcsh and bash
Done to appease the mighty P Taylor.
19 Dec 2018, P Taylor, @djunct_montage_coordinator, level 3 (MAJOR), type 4 (BUG_FIX)
This montage coordinator was noooot picking the right vol to focus on.
That should be fixed via magical incantations now.
14 Dec 2018, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
include mask and params in -csim_show_clustsize
13 Dec 2018, RC Reynolds, @strip.whitespace, level 2 (MINOR), type 1 (NEW_PROG)
stored under scripts_src; guess what it does
11 Dec 2018, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
use mkdir -p; reconcile write_as_nifti and NIFTI prefix
Thanks to C Smith for noting the issue.
10 Dec 2018, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
-cubic12 = use 12 parameter cubics instead of 24
Faster, and probably just as accurate.
05 Dec 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Have removed numpy dependency.
Now, default afni_proc.py will output APQC HTML without numpy on comp.
05 Dec 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 0 (GENERAL)
Have removed numpy dependency.
Lighter installation/usage dependencies.
05 Dec 2018, P Taylor, @djunct_combine_str.py, level 2 (MINOR), type 0 (GENERAL)
Have removed numpy dependency.
Lighter installation/usage dependencies.
05 Dec 2018, P Taylor, @djunct_calc_mont_dims.py, level 2 (MINOR), type 0 (GENERAL)
Have removed numpy dependency.
Lighter installation/usage dependencies.
05 Dec 2018, P Taylor, 1dplot.py, level 2 (MINOR), type 0 (GENERAL)
Have removed numpy dependency.
Lighter installation/usage dependencies.
04 Dec 2018, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
Makefiles: working towards using libmri.so
Pass MRI_SHARED, and apply with SUMA_SHARED_LOPTS in SUMA.
03 Dec 2018, RC Reynolds, test.afni.prog.help, level 2 (MINOR), type 1 (NEW_PROG)
test running -help on AFNI programs
This is a build tool, not for the distribution.
02 Dec 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 4 (BUG_FIX)
Will work with resting state analyses now.
Fixed minor issue when no stat dset (just NO_STATS str) was present.
28 Nov 2018, RW Cox, 3dAllineate, level 2 (MINOR), type 6 (ENHANCE)
Add lpa+ cost functional
Like lpc+, with extra stuff added in for robustness. Per the suggestion
of Daniel Glen, the master of allineation and punulation.
28 Nov 2018, P Taylor, 1dplot.py, level 2 (MINOR), type 4 (BUG_FIX)
In py3, having a censor line caused graphing issues.
Those issues have been resolved.
27 Nov 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 0 (GENERAL)
Now make enorm and outlier plots even if no censor_dsets are in uvars.
Also, on a more fun note, output censor frac below mot/outlier plots.
27 Nov 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL)
Make python3 compatible.
updated.
27 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Wasn't using user's specified delta_slices-- but now is!.
Grazie, S. Torrisi!
26 Nov 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add opt -volreg_warp_final_interp
This controls final interpolation for all non-NN warps, including
catenated EPI transforms (affine and non-linear), final EPI,
and anatomical followers.
Done for "the boss".
25 Nov 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX)
Dsets weren't found in places specified by env var.
Fixed now.
23 Nov 2018, P Taylor, apqc_make_tcsh.py, level 3 (MAJOR), type 0 (GENERAL)
Outputs JSON files now, for easier handling of information later.
These provide more comprehensive info, as well as href linknames.
23 Nov 2018, P Taylor, apqc_make_html.py, level 3 (MAJOR), type 0 (GENERAL)
Much better page formatting now, including navigation bar.
User can jump to sections.
20 Nov 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 0 (GENERAL)
Make subtxt fonts gray (oooh!) and uniformly bold.
Also, made image links not be whole line (much more convenient).
20 Nov 2018, P Taylor, @djunct_montage_coordinator, level 2 (MINOR), type 1 (NEW_PROG)
For use with @chauffeur_afni: subroutine that used to be *in* it.
More modular and useful now, better selection of montage xhair loc, too.
20 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Fixed the calc of the location of xhairs when box_focus_slices was used.
Should have correct focal location in montages now.
19 Nov 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add opt -html_review_style and run apqc_make_html.py
06 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
Fixed delta-slice definition for 4D mode of imaging (occasional probs).
Should have correct gapord values across all views now.
05 Nov 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE)
Alpha and Boxed now work with Clusterize
05 Nov 2018, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 0 (GENERAL)
Adjust to keep up with new afni alpha/boxed behavior.
Update internal calls to @chauffeur_afni, which needed new opts for this.
05 Nov 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-olay_alpha' and '-olay_boxed' for new alpha/boxed driving.
Keepin' up with changes to afni driving, via RWC work.
02 Nov 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE)
Add 'A' and 'B' buttons on top of threshold slider
To control Alpha and Boxed.
01 Nov 2018, P Taylor, 1dplot.py, level 3 (MAJOR), type 1 (NEW_PROG)
New plotting program for 1D files.
Copies much of the fun 1dplot capability to some pythonic realm.
21 Oct 2018, P Taylor, apqc_make_tcsh.py, level 2 (MINOR), type 1 (NEW_PROG)
Helper program for afni_proc.py.
Make @ss_review_html script for HTML version of AP QC.
21 Oct 2018, P Taylor, apqc_make_html.py, level 2 (MINOR), type 1 (NEW_PROG)
Helper program for afni_proc.py.
Run @ss_review_html, build QC dir with html file for ss review.
21 Oct 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-pbar_saveim PBS' and '-pbar_dim PBD', to output color pbar.
Just add in new AFNI driving functionality from RWC, to save colorbar.
19 Oct 2018, RW Cox, AFNI driver, level 2 (MINOR), type 6 (ENHANCE)
Add PBAR_SAVEIM command to the driver repertoire
17 Oct 2018, RW Cox, TSV files, level 2 (MINOR), type 5 (MODIFY)
Replace 'N/A' 'NaN' and 'Inf' with mean of other column values
These strings will no longer stop a column from being marked as 'string'
vs. 'number'.
16 Oct 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added new uvar fields
Move g_ss_uvar_fields to lib_ss_review.py.
Add uvar fields: nt_applied, nt_orig, ss_review_dset,
pre_ss_warn_dset, decon_err_dset, tent_warn_dset.
16 Oct 2018, P Taylor, @FindAfniDsetPath, level 2 (MINOR), type 4 (BUG_FIX)
Maybe not really a bug, but this program wasn't work as it should have.
It now should find NIFTI sets better, and use afnirc env vars.
15 Oct 2018, P Taylor, @djunct_slice_space, level 2 (MINOR), type 1 (NEW_PROG)
Helper program for @chauffeur_afni.
Calculate even spacing of slices for montaging.
15 Oct 2018, P Taylor, @djunct_edgy_align_check, level 2 (MINOR), type 1 (NEW_PROG)
Helper program for @chauffeur_afni-- wrapper of it for QC stuff.
It's for alignment checking, and it's... edgy.
15 Oct 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-box_focus_slices REF', to avoid looking at empty slices.
Can used a masked dset as REF to focus on certain slices only.
15 Oct 2018, P Taylor, 3dAutobox, level 2 (MINOR), type 2 (NEW_OPT)
More new options
Also output midslices, more info to screen (on-demand), and xyz stuff.
15 Oct 2018, P Taylor, 3dAutobox, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-extent_ijk_to_file FF'.
Output IJK extents to a simple-formatted text file.
12 Oct 2018, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
Longname support in AFNI atlases
Environment variable AFNI_ATLAS_NAME_TYPE to control
09 Oct 2018, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
fix decay rest with non-zero min; block unlimited decay stim dur
Thanks to D Plunkett for noting the problem.
05 Oct 2018, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
directly go after expected column headers in TSV files
20 Sep 2018, RW Cox, 3dttest++ etc., level 3 (MAJOR), type 6 (ENHANCE)
ETAC now output global thresholds as well as local
Global thresholds are text tables of cluster-size (or cluster-FOM)
thresholds that apply to the whole volume in the multi-threshold way,
rather than dataset tables that apply voxelwise. Moderately extensive
hanges to programs
3dMultiThresh 3dXClustSim 3dttest++
and to support files
mri_threshX.c thd_Xdataset.c
3dttest++ now has options to turn on/off global and local ETAC threshold
calculations.
28 Aug 2018, P Taylor, @xyz_to_ijk, level 2 (MINOR), type 1 (NEW_PROG)
Helper program to be able to convert xyz coors to ijk indices.
Supplementary program.
27 Aug 2018, RW Cox, 1dsound and AFNI GUI, level 2 (MINOR), type 5 (MODIFY)
modify sound output
1dsound now can make sound from up to 4 columns from input file.
AFNI graph viewer GUI keypresses:
p = play sound from central sub-graph
P = play sound from central and average sub-graph (2 toned)
K = kill running sound player
Note that killing AFNI while sound is playing, or using K to kill sound,
will leave a file whose name is like AFNI_SOUND_TEMP.something.au on the
disk, and the user will have to clean it up.
23 Aug 2018, RW Cox, 1dsound, level 2 (MINOR), type 1 (NEW_PROG)
program to generate .au sound file from a 1D file
Very primitive at this moment.
22 Aug 2018, RC Reynolds, tedana_wrapper.py, level 2 (MINOR), type 5 (MODIFY)
change exec_or_error() to use afni_util.py, which returns strings
Thanks to J Gonzalez-Castillo for noting this python3 update.
20 Aug 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 6 (ENHANCE)
Play sound with 'p' or 'P' keypresses
p = sound from central graph.
P = sound from average of visible graphs.
Sound is played via sox program (not part of AFNI).
Environment variables:
AFNI_SOUND_NOTE_TYPE sets type of note played
AFNI_SOUND_GAIN sets loudness
17 Aug 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -write_uvars_json; add a few more user vars
Add afni_ver, afni_package and final_epi_dset to uvars.
Add 'AFNI version' and 'AFNI package' to review basic output.
Add afni_util:write_data_as_json(), lib_vars_object:get_attribute_dict().
16 Aug 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_computed_uvars; set template
15 Aug 2018, RW Cox, 3dGrayplot, level 3 (MAJOR), type 6 (ENHANCE)
Total rewrite of resampling from time+space to X+Y grid
Grid refinement (time-X) is now cubic interpolation rather than linear
Grid coarsening (space-Y) is now minimum sidelobe taper averaging rather
than linear tapering
15 Aug 2018, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added functions for extracting version information from dataset HISTORY
E.g. get_last_history_ver_pack(), get_last_history_version().
This file now depends on 're'.
14 Aug 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX)
return a zero array on invalid parameters
Thanks to E Silson for noting the problem.
10 Aug 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
Allow non-stat bricks to be thresholded.
Before, if the [ithr] brick was nonstat, crashing occurred.
07 Aug 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if converting tedana.py results to standard space, include -space
Thanks to L Dowdle for noting the problem.
31 Jul 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-check_abs_min ..'.
Just allows the same-named opt from 1dDW_Grad_o_Mat++ to be used.
31 Jul 2018, P Taylor, @GradFlipTest, level 2 (MINOR), type 2 (NEW_OPT)
New opt: '-check_abs_min ..'.
Just allows the same-named opt from 1dDW_Grad_o_Mat++ to be used.
30 Jul 2018, RW Cox, 3dGrayplot, level 2 (MINOR), type 2 (NEW_OPT)
-percent and -range options
For Cesar C-G.
'-range X' sets the values to be plotted over the range -X..X
(black..white).
'-percent' is for plotting non-zero mean files, by converting them to
percent of baseline (mean). Should be combined with '-range 4' (say).
25 Jul 2018, P Taylor, @chauffeur_afni, level 3 (MAJOR), type 0 (GENERAL)
Several new options, as well as ability to deal with 4D images.
Many new features, probably including minor bug fixes.
25 Jul 2018, P Taylor, @djunct_calc_mont_dims.py, level 2 (MINOR), type 4 (BUG_FIX)
Was excluding solution of a square set of dimensions.
Tested; seems fine now.
24 Jul 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE)
version v1.0.20180622, including fix for enhanced DICOM Philips bvec/bval
Update from C Rorden.
23 Jul 2018, RW Cox, AFNI driver, level 2 (MINOR), type 6 (ENHANCE)
New command: SET_ULAY_RANGE
For example: SET_ULAY_RANGE A.axialimage 0 200
05 Jul 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -mask_opts_automask
Done for L Atlas.
01 Jul 2018, P Taylor, @SSwarper, level 3 (MAJOR), type 2 (NEW_OPT)
New opt: well, actually, it is new to *have* explicit options now!
Same great functionality, but with more flexible options/names/outputs.
01 Jul 2018, P Taylor, @snapshot_volreg, level 2 (MINOR), type 0 (GENERAL)
Now respects including a path in the third argument (prefix/filename).
Useful for scripting and selecting directory for output images.
26 Jun 2018, P Taylor, fat_proc_select_vols, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixed in supplementary program to *this* program.
Used to get an error when no bad vols were selected.
26 Jun 2018, P Taylor, fat_proc_convert_anat, level 2 (MINOR), type 2 (NEW_OPT)
Can provide a NIFTI file as input, not just a directory of dicoms.
All niceifying steps can thus be applied to already-converted vol.
26 Jun 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT)
New opt '-focus_by_ss' to do skullstripping before alignment stuff.
Final dset is *not* skullstripped, but it helps with center of mass.
26 Jun 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 4 (BUG_FIX)
Would return an error when *no* bad vols were selected.
Note about fixing it in Jan, 2018; must have forgot to push that ver!
25 Jun 2018, P Taylor, fat_proc_select_vols, level 2 (MINOR), type 0 (GENERAL)
The adjunct program, @djunct_dwi_selector.bash, was changed to be tcsh.
No output diffs; but bash one couldn't run on new Mac OS (bad Mac)...
22 Jun 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE)
version v1.0.20180614, including JPEG-LS support
Update from C Rorden.
21 Jun 2018, RC Reynolds, model_PRF_6_BAD, level 2 (MINOR), type 1 (NEW_PROG)
old model_PRF_6, but with version and gauss_file updates
This is for result comparison.
19 Jun 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 4 (BUG_FIX)
fix rotation term, B should be 2*B
Thanks to R Le, G Usabiaga and B Wandell for suggesting a review.
18 Jun 2018, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 6 (ENHANCE)
add AFNI_MODEL_PRF_GAUSS_FILE env var, to write image of Gaussian
Done for model_conv_PRF and model_conv_PRF_6, should to _DOG, too.
18 Jun 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
more status 0 updates: file_tool, serial_helper
15 Jun 2018, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
update some programs so that -help is valid and return 0
Update 3dGrayplot 3dresample 3dretroicor @2dwarper @FSlabel2dset tokens.
01 Jun 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT)
New pre-alignment opt, -pre_align_center_mass.
Probably more useful than older -pre_center_mass.
01 Jun 2018, P Taylor, 3dLombScargle, level 2 (MINOR), type 0 (GENERAL)
Change scaling of output.
Simpler scaling to match Parseval.
01 Jun 2018, P Taylor, 3dAmpToRSFC, level 2 (MINOR), type 0 (GENERAL)
Adapted to changes of 3dLombScargle.
Simpler scaling to match Parseval.
30 May 2018, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 2 (NEW_OPT)
User can specify matching cost and warp.
How exciting is that?? (Well, mostly for test comparisons...).
29 May 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Can crop the saved images.
See the '-crop_*' options.
27 May 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL)
Make report cleaner, and add in INT_MAP property to output clust map.
Thanks, D. Glen for more useful suggestions.
25 May 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -combine_opts_tedwrap, to pass to tedana_wrapper.py
This is currently for passing -tedana_is_exec, say.
Done for M Vaziri-Pashkam.
24 May 2018, RW Cox, AFNI driver, level 2 (MINOR), type 6 (ENHANCE)
Add SNAP_VIEWER command, for the Neon man.
24 May 2018, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 6 (ENHANCE)
remove any duplicates from merged lists
The 4 categories (accepted/ignored, rejected/midk-rej) might not be
a clean partition.
Thanks to L Dowdle for noting the problem.
23 May 2018, RC Reynolds, get_afni_model_PRF_6, level 2 (MINOR), type 1 (NEW_PROG)
this is just a wrapper for model parameter evaluation
See model Conv_PRF_6 in model_conv_PRF_6.c.
23 May 2018, RC Reynolds, get_afni_model_PRF, level 2 (MINOR), type 1 (NEW_PROG)
this is just a wrapper for model parameter evaluation
See model Conv_PRF in model_conv_PRF.c.
23 May 2018, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -ushort2float
This will add the option to any to3d command via -gert_create_dataset.
Done for H Brice.
23 May 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL)
Some bug fixes if dsets are left out, some new checks on what user asks.
User can't run multi-sided tests on single-sided stats now...
22 May 2018, P Taylor, fat_proc_filter_dwis, level 3 (MAJOR), type 4 (BUG_FIX)
Was unioning, not intersecting, multiple selector strings.
Fixed the issue in subprogram @djunct_combin_str.py.
21 May 2018, P Taylor, p2dsetstat, level 2 (MINOR), type 2 (NEW_OPT)
Include '-bisided' as a type of test, explicitly.
Same behavior as '-2sided', just easier for scripting.
18 May 2018, JK Rajendra, abids_tool.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to modify BIDS datasets.
18 May 2018, JK Rajendra, abids_lib.py, level 4 (SUPER), type 1 (NEW_PROG)
New library to handle data from json files. Useful for BIDS data.
18 May 2018, JK Rajendra, abids_json_info.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to extract data from json files. Useful for BIDS data.
17 May 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 0 (GENERAL)
String subbrick selectors now work for -idat and -ithr.
Also, the text report contains more (useful?) information.
16 May 2018, RC Reynolds, plug_vol2surf, level 2 (MINOR), type 2 (NEW_OPT)
added map_all option for the main 'use vol2surf?' plugin menu
The 'map_all' option applies plugin parameters to all mappable surfaces,
rather than applying defaults to any surface not specified as surf_A/B.
This allows one to use normals and the various mapping functions.
Done for D Glen.
14 May 2018, RC Reynolds, @stim_analyze_modern, level 2 (MINOR), type 1 (NEW_PROG)
added this sample script to doc/misc_scripts
This uses the advanced form of make_random_timing.py.
13 May 2018, P Taylor, 3dClusterize, level 2 (MINOR), type 4 (BUG_FIX)
Wouldn't work with extra dset entered- fixed now.
Can enter extra beta/effect estimate set for clusterizing.
12 May 2018, P Taylor, 3dClusterize, level 3 (MAJOR), type 1 (NEW_PROG)
Perform clusterizing (voxelwise and volume-wise thresholding) on a dset.
Basically like 3dclust but has some new options and easier syntax.
08 May 2018, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
add multi-echo combine methods: OC_tedort, tedana_OC, tedana_OC_tedort
With this, afni_proc.py can run tedana.py and extract projection
components (projecting good orts from bad, making cleaner bad orts).
OC_tedort : like AFNI's OC, but also regress clean orts
tedana_OC : tedana.py's OC
tedana_OC_tedort : tedana.py's OC, and regress clean orts
The tedort (orthogonalized tedana projection components) terms are
applied in the regress block, still as per-run terms.
08 May 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
3dQwarp warp datasets need only be named _WARP
Thanks to dowdlelt on MB for bringing this up.
07 May 2018, RW Cox, @grayplot, level 2 (MINOR), type 1 (NEW_PROG)
Script to drive 3dGrayplot in afni_proc.py output directory
Will grayplot errts* and all_runs datasets, with motion indicator graph
and (if available) sum_ideal.1D graph.
07 May 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
EPI automask (full_mask) is no longer dilated by default
Also, add -show_process_changes, to report changes affecting results.
07 May 2018, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 2 (NEW_OPT)
add -ver, -meica_dir, -work_dir, init history
04 May 2018, JK Rajendra, BayesianGroupAna.py, level 4 (SUPER), type 1 (NEW_PROG)
New program to perform Bayesian group analysis on ROI level data.
03 May 2018, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 1 (NEW_PROG)
new program to extract MEICA projection vectors
These 'rejected' terms are orthogonalized to the 'accepted' ones.
This was written to be called by afni_proc.py.
28 Apr 2018, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT)
add option -stop_gap and map functions nzave, nzmode, median, nzmedian
26 Apr 2018, DR Glen, ORIG space, level 2 (MINOR), type 0 (GENERAL)
ORIG space formally defined in AFNI_atlas_spaces.niml
Should allow for FreeSurfer segmentation to be used
with the SessionAtlases.niml created by @SUMA_MakeSpecFS
This change currently applies only to the whereami command
line. The afni GUI still requires a +tlrc or equivalent view.
26 Apr 2018, DR Glen, @surf_to_vol_spackle, level 2 (MINOR), type 1 (NEW_PROG)
propagate surface to volume and fill holes
25 Apr 2018, RC Reynolds, meica.py, level 2 (MINOR), type 4 (BUG_FIX)
deal with numpy update that fails for 'array == None', use 'is None'
Thanks to dowdlele on MB for noting this and pointing to the emdupre
update on https://github.com/ME-ICA/me-ica.
25 Apr 2018, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 1.0
24 Apr 2018, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 0.4
24 Apr 2018, RC Reynolds, auto_warp.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 0.4
22 Apr 2018, P Taylor, 3dSliceNDice, level 3 (MAJOR), type 1 (NEW_PROG)
Calculate Dice coefficients between volumes on a slicewise basis.
Useful for comparing masks/maps of volumes.
22 Apr 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 4 (BUG_FIX)
When using '-remove_inf_sli', the wrong volume was being warped at end.
Final warped volume had lower slice reduction, when it shouldn't have.
18 Apr 2018, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -csim_show_clustsize and helper options to report cluster requirements
Given a cluster table output by 3dClustSim, use this option to extract
the minimum cluster size, given uncorrected and corrected p-values.
Use -csim_pthr and -csim_alpha to specify those respective p-values.
16 Apr 2018, P Taylor, p2dsetstat, level 3 (MAJOR), type 1 (NEW_PROG)
Program to convert a p-value to a statistic, using params in dset header.
Useful to calculate thresholds for a particular volume.
12 Apr 2018, RC Reynolds, dcm2niix_afni, level 3 (MAJOR), type 6 (ENHANCE)
version v1.0.20180403, including support for Philips enhanced DICOMs
Update from C Rorden.
09 Apr 2018, RW Cox, 3dGrayplot, level 2 (MINOR), type 1 (NEW_PROG)
A plot, a la JD Power, of time series intensities in a brain mask
For Cesar Caballero-Gaudes, and anyone else who actually cares about
data quality.
04 Apr 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -combine_opts_tedana, to pass opts down to tedana.py
03 Apr 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
initial testing run with -combine_tedana_path
28 Mar 2018, RW Cox, 3dNwarpApply, level 3 (MAJOR), type 6 (ENHANCE)
Program now warps complex-valued datasets.
Real and imaginary parts are extracted, warped, and combined.
No special option is needed.
23 Mar 2018, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Add 3dTstat pseudo-plugin on the Insta-stuff menu
Calculate voxelwise statistics of 3D+time datasets. Works by running
3dTstat. A few changes to 3dTstat to make this easier, as well.
23 Mar 2018, JK Rajendra, tedana_wrapper.py, level 4 (SUPER), type 1 (NEW_PROG)
add wrapper for tedana.py that will be run from afni_proc.py
19 Mar 2018, RW Cox, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
Add -MSSD and -MASD option
MSSD = mean successive squared differences (Von Neumann)
MASD = median absolute successive differences
15 Mar 2018, P Taylor, fat_proc_convert_dwis, level 2 (MINOR), type 2 (NEW_OPT)
Can provide NIFTI+bvec+bval files as inp, not just a directory of dicoms.
All niceifying steps can thus be applied to already-converted vol.
14 Mar 2018, P Taylor, fat_proc_filter_dwis, level 2 (MINOR), type 4 (BUG_FIX)
Crashed when b-value file was input.
Crashes no more under such circumstance.
14 Mar 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 4 (BUG_FIX)
Crashed no ref dset was used in mapping.
Crashes no more under such circumstance.
06 Mar 2018, P Taylor, fat_proc_convert_dwis, level 2 (MINOR), type 5 (MODIFY)
Default orientation for nifti files to be 'RAI' instead of 'RPI'.
This will be more in line with TORTOISE (and AFNI DICOM-coor default).
06 Mar 2018, P Taylor, fat_proc_convert_anat, level 2 (MINOR), type 5 (MODIFY)
Default orientation for nifti files to be 'RAI' instead of 'RPI'.
This will be more in line with TORTOISE (and AFNI DICOM-coor default).
05 Mar 2018, JK Rajendra, FATCAT_matplot, level 2 (MINOR), type 0 (GENERAL)
changed name of @FATCAT_heatmap_shiny to FATCAT_matplot
01 Mar 2018, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT)
add -oc_method (OC_A, OC_B)
OC_B: compute T2* from full log() time series, rather than log(mean(TS)).
26 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -help_section, and use it to add some missing option help
23 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add option for running OC combine method, use '-combine_method OC'
This will run the current method implemented in @compute_OC_weights.
This is probably a bit of a test, as I expect to modify the base 'OC'
method, and therefore add other related names.
23 Feb 2018, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT)
add option -echo_times, for convenient use by afni_proc.py
22 Feb 2018, RC Reynolds, 3dMean, level 2 (MINOR), type 2 (NEW_OPT)
add option -weightset to compute a weighted sum
This N-volume weight dataset is used to apply voxelwise weights to the N
input datasets, one volumetric weight to each dataset. The motivated
example is combining single runs (at a time) of multi-echo data with the
weights generated by @compute_OC_weights.
22 Feb 2018, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Can now apply p-to-stat calcs for thresholding.
User gives p-value, which gets made to appropriate stat for thresh.
16 Feb 2018, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
add combine block and ability to process multi-echo data
Have new options -dsets_me_echo and -dsets_me_run for input.
Still need to implement OC and ME-ICA.
Thanks to L Atlas and J Gonzalez-Castillo.
16 Feb 2018, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -mask_epi_anat, to apply tigher mask in place of full_mask
By default, create epi_anat intersection mask.
15 Feb 2018, RC Reynolds, @compute_OC_weights, level 3 (MAJOR), type 1 (NEW_PROG)
compute voxelwise weights for optimally combining multi-echo data
The equations are based on the summer 2017 talk by J Gonzalez-Castillo.
13 Feb 2018, P Taylor, fat_proc_filter_dwis, level 2 (MINOR), type 5 (MODIFY)
Can now accept *multiple* selector strings that get merged.
Multiple strings/files can be input, yay.
08 Feb 2018, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 4 (BUG_FIX)
When a mask was input, it wasn't resampled if needed to be.
Now fixed, and added check that grid of mask is good. Good.
06 Feb 2018, P Taylor, fat_proc_axialize_anat, level 2 (MINOR), type 2 (NEW_OPT)
Can put a ceiling on the final output volume: -do_ceil_out.
Reduce impact of tiny spikes (often at fringe) later on.
02 Feb 2018, RW Cox, AFNI GUI, level 2 (MINOR), type 5 (MODIFY)
Read .jpg and .png 'datasets' by default into sessions
01 Feb 2018, RW Cox, AFNI GUI, level 3 (MAJOR), type 2 (NEW_OPT)
-bysub option for reading from BIDS hierarchy
-bysub 10506 (for example) means to find all sub-directories with names
'sub-10506', and read all datasets find in them and in THEIR
sub-directories into a single session. The idea is to make it easy to
read all datasets corresponding to a single subject from a BID hierarchy
into a single session, for easy of viewing.
01 Feb 2018, RC Reynolds, 3dTto1D, level 2 (MINOR), type 2 (NEW_OPT)
add methods 4095_count/frac/warn
Count 4095 values, or warn if datum is short and max is 4095.
01 Feb 2018, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
Internal change to allow subset selection in text files.
Can now use subbrick selector notation with bvals/bvecs.
26 Jan 2018, JK Rajendra, dicom_hinfo, level 2 (MINOR), type 0 (GENERAL)
add -full_entry
prints out the full entry of a tag if there are more than one word
18 Jan 2018, DR Glen, thickness scripts, level 4 (SUPER), type 1 (NEW_PROG)
Scripts to compute thickness of a mask 3 ways
@measure_bb_thick, @measure_erosion_thick, @measure_in2out
Suite of thickness scripts to compute thickness in volume
and map to surface. Master script, @thickness_master, to
call others with option for FreeSurfer input data
12 Jan 2018, P Taylor, @djunct_select_str.py, level 2 (MINOR), type 4 (BUG_FIX)
Would return an error when *no* bad vols were selected.
Now updated to work fine with that; just an intermed program.
06 Jan 2018, RW Cox, 3dDeconvolve, level 2 (MINOR), type 6 (ENHANCE)
Add TWOGAM basis function
Arbitrary difference of two GAM functions.
02 Jan 2018, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 1.0
Also, add -write_text_data for L Morris and D Huynh.
29 Dec 2017, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 1.0
28 Dec 2017, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 2.0
28 Dec 2017, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 1.0
22 Dec 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -select_runs and -mplaces
For B Benson and A Harrewijn, see Example 18d.
22 Dec 2017, P Taylor, fat_proc_connec_vis, level 2 (MINOR), type 2 (NEW_OPT)
Can output the intermediate tstat or tcat files of ROI maps.
Might be useful in subsequent volumetric analyses.
20 Dec 2017, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Add driver command DATASET#N
To let the user drive the graph viewer plugin from outside. A little
trickier than I thought, since to do this well requires mucking with the
menu settings inside afni_graph.c as well as registering a new driver
function in plug_nth_dataset.c.
20 Dec 2017, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Increase the maximum dimension of an image Montage (for PT)
20 Dec 2017, RW Cox, 3drefit, level 2 (MINOR), type 2 (NEW_OPT)
-Tslices lets user replace slice time offsets
I don't know why this didn't exist before. So now the user can attach
slice time offsets to a dataset if they weren't correct before (e.g., in
NIFTI files).
20 Dec 2017, RW Cox, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Make -substatpar option work better
It didn't work on some datasets, as they weren't labeled as 'bucket'.
That oversight was fixed.
20 Dec 2017, P Taylor, fat_proc_connec_vis, level 2 (MINOR), type 5 (MODIFY)
Changing the way that outputting is specified.
Make making a separate directory the default output; new opt for files.
19 Dec 2017, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
uniq_list_as_dsets: (def) no restriction to prefix; dmUBLOCK known basis
29 Nov 2017, P Taylor, @djunct_4d_imager, level 3 (MAJOR), type 1 (NEW_PROG)
Helper function to make montages and movies of 4D dsets.
Useful when proc'ing dsets, make record of them.
21 Nov 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
add options -not_first and -not_last, to block tasks at run boundaries
For C Smith.
15 Nov 2017, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
-despike_mask had been tested with wrong option name
Fix submitted by D Plunkett.
09 Nov 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 3.00
09 Nov 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 3.0
07 Nov 2017, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
python3 compatible as of version 6.00
07 Nov 2017, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 1.00
07 Nov 2017, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
python3 compatible as of version 2.00
06 Nov 2017, RC Reynolds, afni-general, level 3 (MAJOR), type 6 (ENHANCE)
first stab at making python program p2/p3 compatible
Based on 2to3 and dglen mods, and tested in p2 and p3 environments.
01 Nov 2017, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 2 (NEW_OPT)
implement the decay_fixed distribution type
See make_random_timing.py -help_decay_fixed for details.
31 Oct 2017, RW Cox, 3dMultiThresh, level 2 (MINOR), type 2 (NEW_OPT)
Add -allmask option, to see which case(s) caused a positive
Add then used in 3dttest++ to produce the ETACmaskALL output dataset
26 Oct 2017, P Taylor, fat_proc_connec_vis, level 3 (MAJOR), type 1 (NEW_PROG)
Visualize 'white matter connection' volumes output by 3dTrackID.
Combine separate '-dump_rois ...' output into SUMAble surface maps.
25 Oct 2017, JK Rajendra, @afni_R_package_install, level 4 (SUPER), type 1 (NEW_PROG)
add new program @afni_R_package_install
Will install R libraries to run shiny apps
12 Oct 2017, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
Change output formatting and getting basename of prefix name.
Easier output and reading in terminal/files.
11 Oct 2017, JK Rajendra, ClustExp_StatParse.py, level 4 (SUPER), type 1 (NEW_PROG)
add new program ClustExp_StatParse.py
Part of cluster explorer. Extract subject level data from clusters and
output tables and a shiny app
11 Oct 2017, JK Rajendra, ClustExp_HistTable.py, level 4 (SUPER), type 1 (NEW_PROG)
add new program ClustExp_HistTable.py
Part of cluster explorer. Extract data tables from the history of datasets
11 Oct 2017, JK Rajendra, @FATCAT_heatmap_shiny, level 4 (SUPER), type 1 (NEW_PROG)
add new program @FATCAT_heatmap_shiny
Run a shiny app to view .netcc or .grid files
11 Oct 2017, JK Rajendra, @ClustExp_run_shiny, level 4 (SUPER), type 1 (NEW_PROG)
add new program @ClustExp_run_shiny
Part of cluster explorer. Run the shiny app output from ClustExp_StatParse
.py
11 Oct 2017, JK Rajendra, @ClustExp_CatLab, level 4 (SUPER), type 1 (NEW_PROG)
add new program @ClustExp_CatLab
Part of cluster explorer. Concatenates and labels input datasets
04 Oct 2017, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
Change the output directory naming/choosing options.
Do more with just '-prefix ...', in standard AFNI fashion.
29 Sep 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 5 (MODIFY)
Now has help with list of options.
Should be useful for users during processing.
26 Sep 2017, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE)
Make -zskip work nicely with -resid
22 Sep 2017, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 4 (BUG_FIX)
On Macs, when not all types of 'follower' sets were used, this gave err.
Have changed internal behavior to avoid this 'Mac'errorizing.
20 Sep 2017, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 2 (NEW_OPT)
New opt to push through tiny, negative diagonal elements in bmatrices.
Useful-- but use this option cautiously, and look at your data...
19 Sep 2017, P Taylor, 3dLombScargle, level 2 (MINOR), type 4 (BUG_FIX)
delF calculated correctly now.
Had been at N-1 instead of N. Better Parsevalling now.
15 Sep 2017, RW Cox, 1dplot, level 2 (MINOR), type 6 (ENHANCE)
Allow -xaxis to have bot > top, so x decreases from left to right
14 Sep 2017, P Taylor, 3dLombScargle, level 3 (MAJOR), type 4 (BUG_FIX)
Finally revisiting this-- fixed up lots of things.
Good to go for basic functionality now.
12 Sep 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -multi_timing_3col_tsv and -write_multi_timing
Also, add -multi_show_duration_stats for married timing files.
This is to process 3 column TSV (tab separated value) formatted timing
files, as might be found in the OpenFMRI data.
11 Sep 2017, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
if no regress block, omit gen_ss_review_scripts.py
06 Sep 2017, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
allow user control of registration and plots with multi-chan/echo data
This previously required channel merging or registering.
For W Luh.
06 Sep 2017, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
re-apply cleaner xim use, so end of run signal has full image size
Short end of run was hanging afni, but was not noticed since the
communication was immediately terminated. Fixes multi-run use.
06 Sep 2017, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 5 (MODIFY)
Output a couple more types of QC images by default.
Output b0 ulay with anat-edge olay; also, some uncert images.
06 Sep 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 5 (MODIFY)
Now gets output path as part of '-prefix' as opposed to sep '-outdir'.
Now in line with most of AFNI funcs.
30 Aug 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -fsl_timing_files and -write_as_married
This is for converting FSL timing files to AFNI format.
24 Aug 2017, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
The file storing the flip recommendation will *overwrite* a previous one.
Previous version of this would *append to*, which seems pointless.
23 Aug 2017, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE)
All 'fpr=ALL' in -ETAC_opt
To let user get results for FPR goals from 2-9 percent.
22 Aug 2017, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -apply_end_times_as_durations and -show_duration_stats
For B Benson and P Vidal-Ribas.
17 Aug 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Some new labelling, etc. optioning.
Make some new labels, locationing based on XYZ and more.
11 Aug 2017, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 5 (MODIFY)
Make range associated with ROI map images =256 for all.
This provides better consistency in coloration with ROI_i256 cbar.
11 Aug 2017, P Taylor, fat_proc_align_anat_pair, level 2 (MINOR), type 5 (MODIFY)
Change a '>>' to '>' for wider compatibility.
Yup.
08 Aug 2017, P Taylor, fat_proc_map_to_dti, level 2 (MINOR), type 2 (NEW_OPT)
Can have surfaces, niml.dsets and spec files move along with vols.
Added capability to mapping volume dsets.
08 Aug 2017, P Taylor, @suma_reprefixize_spec, level 2 (MINOR), type 1 (NEW_PROG)
Helper function to copy a spec file whilst renaming files inside.
Useful when copying a lot of *.gii or other surface files.
04 Aug 2017, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
-ETAC failed without multiple blur cases
Addition of -ETAC_blur broke the non-blur runs, due to lack of the
correct 'label' for dealing with the results from 3dXClustSim.
Obviously, this was the work of saboteurs.
02 Aug 2017, RW Cox, 3dBrainSync, level 3 (MAJOR), type 1 (NEW_PROG)
BrainSync algorithm of Joshi, from OHBM 2017
Also, my own permutation method (to avoid linear combination of
disparate time points).
01 Aug 2017, P Taylor, fat_proc_dwi_to_dt, level 2 (MINOR), type 5 (MODIFY)
Turn on reweighting and cumulative weight calc in 3dDWItoDT part.
More useful fitting+output, hopefully.
01 Aug 2017, P Taylor, 3dDWItoDT, level 2 (MINOR), type 5 (MODIFY)
Have the '-cumulative_wts' output also get dumped into a 1D file.
Figured it was nice to not *only* have info in the terminal.
24 Jul 2017, RC Reynolds, nifti_tool, level 2 (MINOR), type 5 (MODIFY)
treat ANALYZE more as NIFTI-1; apply more PRId64 macros for I/O
20 Jul 2017, RW Cox, 3dFWHMx, level 3 (MAJOR), type 2 (NEW_OPT)
Require -ShowMeClassicFWHM to get the Forman FWHM estimates
Otherwise, these results are shown only as zeros. The intention is to
make it harder to use an archaic model for the noise spatial
correlation. But not to break afni_proc.py, which expects 4 values to
be output there.
19 Jul 2017, RC Reynolds, 3dTto1D, level 3 (MAJOR), type 1 (NEW_PROG)
time series to 1D : e.g. compute enorm, DVARS(RMS), SRMS
Given time series data such as EPI or motion parameters, compute
things like Euclidean norm and RMS (a.k.a. DVARS).
13 Jul 2017, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT)
Add '-NNx' options to specify clustering method
-NN1 or -NN2 or -NN3
These can replace the use of 'rmm' and 'vmul', and are meant
to make using this program simpler and more compatible with
Clusterize in the AFNI GUI.
03 Jul 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 2 (NEW_OPT)
Some new subbrick-setting optioning.
For utilizing 'SET_SUBBRICKS i j k' functionality in driving afni.
28 Jun 2017, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL)
add afni_src/other_builds files for Fedora 25 (Makefile, OS_notes)
07 Jun 2017, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 5 (MODIFY)
Added two more FS 'undetermined' regions to the list, ROIs 29 and 61.
One voxel of one was in one subject once. Joy. Now part of tiss__unkn.
06 Jun 2017, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT)
New inflation opt: '-skel_stop_strict'.
Think this might be useful: don't expand at all *into* WM skel.
05 Jun 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
peak_finder(): fix lengths of r['t'] and r['tR']
Be more cautious with ratios that are very close to integers.
05 Jun 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
merge phase_base() fix by D Nielson
range() is closed in matlab but half-open in python.
02 Jun 2017, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
add Makefile.linux_ubuntu_16_64 and OS_notes.linux_ubuntu_16_64
This is for setting up an Ubuntu 16 build machine.
26 May 2017, P Taylor, 3dReHo, level 2 (MINOR), type 4 (BUG_FIX)
Correct checking for null time series now.
Earlier, only looked at [0]th point; now sums across all.
26 May 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 4 (BUG_FIX)
Correct checking for null time series now.
Earlier, only looked at [0]th point; now sums across all.
25 May 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
can now apply -save_3dd_cmd and -make_3dd_contrasts in advanced case
Advanced usage can generate 3dDeconvolve command scripts, with contrasts.
16 May 2017, RC Reynolds, meica.py, level 2 (MINOR), type 6 (ENHANCE)
sync with https://bitbucket.org/prantikk/me-ica/src
Update from version 2.5 beta9 to 2.5 beta11.
12 May 2017, P Taylor, 3dDWItoDT, level 3 (MAJOR), type 2 (NEW_OPT)
Added goodness-of-fit measures to '-debug_brik' output.
Two chi-sqs from Papadakis et al. (2003); thx, J Ipser for idea.
11 May 2017, P Taylor, 3dDTtoDWI, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed mismatch in multiplying DT and bmatrices.
Element indices hadn't been sync'ed, now they are.
10 May 2017, RC Reynolds, model_conv_PRF_DOG, level 2 (MINOR), type 1 (NEW_PROG)
new model: same as PRF, but Difference of Gaussians
For E Silson and C Baker.
09 May 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
apply -offset for advanced case (remove from todo list)
04 May 2017, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT)
Allow box-y neighborhoods.
User can input values for cubic/prism neighborhoods now.
04 May 2017, P Taylor, 3dDTtoDWI, level 2 (MINOR), type 2 (NEW_OPT)
Added in '-scale_out_1000' option, to match 3dDWItoDT.
This allows it to be used with scaled tensors from 3dDWItoDT.
03 May 2017, RW Cox, Historical Records, level 2 (MINOR), type 6 (ENHANCE)
Add the AFNI version to the History Note for new datasets
So the user can see (via 3dinfo) exactly what version created a dataset.
03 May 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 5 (MODIFY)
The opacity in olays wasn't working with xvfb-run-- now it does.
Pixel depth was not useful by default, I think.
02 May 2017, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
properly handle column major order
Convert to row major order on read; can control with gifti_tool.
Thanks to JH Lee for noting the problem.
01 May 2017, RC Reynolds, @diff.files, level 2 (MINOR), type 2 (NEW_OPT)
add option -diff_prog, to use something besides xxdiff
27 Apr 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
With '-output_mask_nonnull', user can output mask of non-null ts.
This was made to help those who need to finnd null time series here.
27 Apr 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
With '-ts_wb_strlabel', can use ROI string labels in WB output filenames.
This was made expressly for The Rajendra Who Shall Not Be Named.
27 Apr 2017, P Taylor, 3dNetCorr, level 2 (MINOR), type 5 (MODIFY)
More watchfulness for null time series from badly masked dsets.
Count and report null time series, and possibly fail if too many.
25 Apr 2017, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
no COL_MAJOR changes for gifti_DA_rows_cols, write_*_file
Also, init gifti_globs_t struct with verb=1.
21 Apr 2017, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE)
Extensive modifications to ETAC
Adding the ability to due multiple amounts of blurring. Some changes to
3dttest++ and 3dMultiThresh, big changes to 3dXClustSim.
19 Apr 2017, DR Glen, 3dMean min, max options, level 2 (MINOR), type 2 (NEW_OPT)
3dMean computes min and max voxelwise across datasets
Options -min, -max give min and max values. This can be
combined with -non-zero to restrict to non-zero min and max.
19 Apr 2017, DR Glen, 3dLocalstat has_mask, has_mask2 options, level 2 (MINOR), type 2 (NEW_OPT)
3dLocalstat can report if neighborhood intersects specified values
Options -has_mask and -has_mask2 allow flagging with unfillvalue
12 Apr 2017, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
in suggest_best_prog_option(), do not search for -help, -h_* or similar
A program without -help that tests it would otherwise lead to an
infinitely recursive system call trying to use -help to suggest an option.
10 Apr 2017, JK Rajendra, 3dTstat, level 2 (MINOR), type 0 (GENERAL)
add -tsnr
same as -cvarinvNOD
05 Apr 2017, DR Glen, 3dVol2Surf nzoptions, level 2 (MINOR), type 2 (NEW_OPT)
3dVol2Surf nonzero min, nonzero max, nonzero ave
Options allowing for statistics that ignore zero values
30 Mar 2017, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
simple statistics of filled or unfilled
These options provide binary tests for whether the neighborhood shape
entirely fits within a mask or dataset around each voxel
A value can be specified for a fill and unfill value
29 Mar 2017, JK Rajendra, prompt_popup, level 2 (MINOR), type 1 (NEW_PROG)
add new program prompt_popup
Similar to prompt_user, but adds label customization and up to 3 buttons
27 Mar 2017, RC Reynolds, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
add -write_dist, for writing a distortion vector dataset
After running something like:
MapIcosahedron ... -write_dist test.dist
to create test.dist.lh.sphere.reg.gii.txt, get summaries with:
1d_tool.py -collapse_cols euclidean_norm -show_mmms \
-infile test.dist.lh.sphere.reg.gii.txt
27 Mar 2017, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
rm of temporary files could delete all files in current directory
rm deletes all files that have tabs/spaces inserted in dataset names
The tab or space character can be somewhat invisible if after
line continuation character in input script. Fix removes whitespace
before deleting
21 Mar 2017, RC Reynolds, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
fix projection of surfaces with non-zero centers
Center each surface around 0,0,0 instead of leaving the offset in.
Many thanks go to I Dewitt for even noticing this subtle issue,
much less diagnosing where it might be coming from. Not easy.
16 Mar 2017, RW Cox, 3dttest++, level 2 (MINOR), type 6 (ENHANCE)
-Clustsim option now also output 5 percent points for global z-stat
Takes the global min/max of the randomized z-stat results for each
iteration (10000) and then computes the 5 percent points for the
1-sided and 2-sided cases. Is this useful? Maybe for somebody.
07 Mar 2017, RC Reynolds, RetroTS.py, level 2 (MINOR), type 4 (BUG_FIX)
from J Zosky: default to using numpy.flipud()
The flipud() function did not work in the original Matlab version,
but it does in numpy. Use the new -legacy_transform opt for old
(and presumably incorrect) results.
03 Mar 2017, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
add optimally combined 'Opt Comb' merge method
Done with V Roopchansingh.
01 Mar 2017, RW Cox, 3dUnifize, level 3 (MAJOR), type 2 (NEW_OPT)
Add -EPI option, to unifize time series datasets.
20 Feb 2017, RW Cox, 3dDespike, level 2 (MINOR), type 4 (BUG_FIX)
Scale factor bug
The program ignored the scale factors attached to short datasets.
If they were all the same, that was not a problem.
But if they differed, then that was a big problem.
That was fixed. Also, the output now is always in float format.
09 Feb 2017, RW Cox, thresholding, level 2 (MINOR), type 3 (NEW_ENV)
Fix inconsistency in thresholding with short-valued bricks
In the AFNI GUI, thresholding is done with floats.
But in 3dmerge and in Clusterize, if the thresh brick is a short,
thresholding was done with shorts. And the user-supplied threshold was
ROUNDED -- so that a threshold of 2.2 would become 2, which means that a
value of 2 was OK -- which it shouldn't be. Solution: change those
places to threshold with floats. However, if someone wants to keep the
old way for compatibility, then they can set AFNI_OLD_SHORT_THRESH to
YES.
06 Feb 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 5 (MODIFY)
Should deal with subbrick selection now.
Works for ulay and olay sets in usual AFNI way.
03 Feb 2017, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
decay timing class now follows better distribution; new decay_old class
02 Feb 2017, RC Reynolds, steps_mac.rst, level 2 (MINOR), type 5 (MODIFY)
rewrite OS X install instructions to use 10.7_local and fink
01 Feb 2017, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
updates for fink and homebrew
31 Jan 2017, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 5 (MODIFY)
Update region list to work with new FS 6.0 that came out a week ago.
Regions #3 and #42 (in FS file output) appear now; ~'leftover' GM.
27 Jan 2017, P Taylor, @GradFlipTest, level 3 (MAJOR), type 5 (MODIFY)
Totally revamped-- have real options, better funcs, output text file.
Meshes with other changes in 1dDW_Grad* and 3dDWItoDT.
26 Jan 2017, RC Reynolds, Makefile.macosx_10.7_local, level 2 (MINOR), type 2 (NEW_OPT)
this is a new Makefile to prep for exec directory dynamic linking
26 Jan 2017, P Taylor, @chauffeur_afni, level 2 (MINOR), type 1 (NEW_PROG)
Simplish function for driving AFNI to make images/montages.
Based on @snapshot_volreg; mainly intended for my selfish use.
26 Jan 2017, P Taylor, 1dDW_Grad_o_Mat++, level 2 (MINOR), type 1 (NEW_PROG)
New program for changing/reformatting grads and things.
Better defaults and simpler than original 1dDW_Grad_o_Mat++.
25 Jan 2017, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
in 10.11+, check for DYLD variables via sub-shells
20 Jan 2017, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 6 (ENHANCE)
advanced usage, program version 2.00
Essentially a new program. The user may now define timing classes for
stimulus and rest event types.
see: make_random_timing.py -help_advanced
Motivated by K Kircanski and A Stringaris.
05 Jan 2017, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI output and output directories not always handled correctly or completely
30 Dec 2016, P Taylor, @SUMA_renumber_FS, level 2 (MINOR), type 1 (NEW_PROG)
New program for renumbering FS output after @SUMA_Make_Spec_FS.
Also conglomerates things into tissue maps.
30 Dec 2016, P Taylor, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY)
Output new data sets of renumb'd values, more consistent than 'rank' ones.
Also output more tissue segmentation maps based on ROIs.
29 Dec 2016, RW Cox, @SSwarper, level 2 (MINOR), type 1 (NEW_PROG)
New script to combine skull stripping and nonlinear warping
Uses partial warping to improve skull stripping, and then finishes the
warping, producing outputs compatible for use with afni_proc.py
-tlrc_NL_warped_dsets
26 Dec 2016, P Taylor, thd_center, level 2 (MINOR), type 2 (NEW_OPT)
Extra argument in THD_cmass() and THD_roi_cmass().
Allows for local ijk coordinate output; updated other calling functions.
23 Dec 2016, P Taylor, 3dCM, level 2 (MINOR), type 2 (NEW_OPT)
Allow ijk coordinate output.
Will be in local orientation. Makes undumping after easier.
21 Dec 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
Add '-wmask' option
Like '-wball', enhances the auto-generated weight in a region, but this
region is selected by a mask dataset.
08 Dec 2016, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 2 (NEW_OPT)
add -digits and -keep_datum; other minor updates
08 Dec 2016, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 1 (NEW_PROG)
program to break 4D dataset into a set of 3D ones
Authored by P Molfese.
30 Nov 2016, RC Reynolds, afni-general, level 3 (MAJOR), type 6 (ENHANCE)
<> range selector can now take a comma-delimited list of integers
So for a dataset with integer values from 0 to 8, these commands
should produce identical results:
3dcalc -a DSET+tlrc -expr 'a*amongst(a,3,4,5)' -prefix JELLO
3dbucket 'DSET+tlrc<4,3,5>' -prefix JELLO
3dbucket 'DSET+tlrc<3..5>' -prefix JELLO
3dbucket 'DSET+tlrc<2.3..5.86>' -prefix JELLO
Of course, this will probably get further enhanced to a list of
float ranges. We shall see.
Comma-delimited labels should work now, with a plan to add general
labels that might define all GM or similar in a FreeSurfer dataset, say.
23 Nov 2016, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Used to be able to have nans in sBL b/c of sqrt(neg-from-rounding).
Now IF condition to prevent that. Happy Thanksgiving.
23 Nov 2016, P Taylor, 3dNetCorr, level 2 (MINOR), type 4 (BUG_FIX)
Z-score WB maps were all zeros-> now have values.
Hopefully even the correct Z-values.
17 Nov 2016, DR Glen, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Ask suma to send current surface name to SUMA_OUTPLUG file or stdout
16 Nov 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 0 (GENERAL)
Check for singular values, so don't get crashes from GSL calcs.
These pretty much occur outside mask, but can also be inside mask.
16 Nov 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 0 (GENERAL)
Output b-values are now floats, not ints.
Seems necessary, depending on what user has input.
16 Nov 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 4 (BUG_FIX)
The -out_bval_col_sep used did nothing (after last changes).
Have returned it to functionality.
08 Nov 2016, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
possibly invert slice order, as DICOM sorting might affect MRILIB_orients
Thanks to W Luh for noting the problem.
07 Nov 2016, RW Cox, 3dTfilter, level 2 (MINOR), type 1 (NEW_PROG)
Platform for generic filtering of time series
Right now, just for adaptive local mean filtering (generalized smoothing
plus despiking).
04 Nov 2016, RW Cox, afni InstaCorr, level 2 (MINOR), type 6 (ENHANCE)
Two small changes
(1) Extend the range of the bandpass to allow up to 10Hz (formerly only
up to 1Hz). 10Hz = Nyquist frequency for TR=0.05s, which is pretty fast
for MRI -- but doable for single slice imaging.
(2) Add a #PC option, to compute principal components to use as global
orts.
01 Nov 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add PPI preparation options
Add -regress_skip_censor to omit 3dD -censor option.
Add -write_ppi_3dD_scripts with corresponding options
-regress_ppi_stim_files and -regress_ppi_stim_labels.
These make PPI pre and post regression scripts, along with
the main analysis script.
Done for S Haller.
13 Oct 2016, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fix -BminusA bug
double sign reversal == no sign reversal == not good for anyone
12 Oct 2016, RC Reynolds, RetroTS.py, level 3 (MAJOR), type 1 (NEW_PROG)
distribute RetroTS.py (RetroTS.m converted to python)
This should behave almost exactly as the MATLAB version.
See 'RetroTS.py -help' for details.
Much thanks to J Zosky for this contribution!
12 Oct 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 0 (GENERAL)
Now output progress; also, only divvy up non-zeros to proc.
Should be faster/better parallelized, also tell user about itself.
12 Oct 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 0 (GENERAL)
Now, automatically output RD if '-eigs' opt is used.
And the users of 3dTrackID say, 'Yaaaay'. Or 'Wha'evah!'.
11 Oct 2016, P Taylor, 3dDWUncert, level 3 (MAJOR), type 0 (GENERAL)
Totally reprogrammed, mainly to use OpenMP and be fstr.
Also should be more generalized if b0 != 0.
09 Oct 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
new options -mask_import, -mask_intersect and -mask_union
For J Stoddard and J Jarcho.
05 Oct 2016, RC Reynolds, afni-general, level 3 (MAJOR), type 1 (NEW_PROG)
update from C Craddock and dclark87
New Programs: 3dLFCD, 3dDegreeCentrality, 3dECM, 3dMSE, 3dsvm_linpredict.
30 Sep 2016, RW Cox, AFNI plugins, level 3 (MAJOR), type 0 (GENERAL)
A long list of little-used plugins has been disabled.
They can all be re-enabled by setting environment variable
AFNI_ALLOW_ALL_PLUGINS to YES.
Or each one can be individually re-enabled by setting environment
variable AFNI_ALLOW_somename_PLUGIN to YES, where the list of such
plugins can be found in file README.environment.
29 Sep 2016, RW Cox, 3dDespike, level 2 (MINOR), type 2 (NEW_OPT)
-NEW25 is a slightly more aggressive approach
(a) uses 25 point running median instead of 9 for pre-filtering
(b) sets cut2=3.2 (4 MADs) instead of 4.0 (5 MADs)
28 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -regress_ROI[_PC]_per_run options, to make per-run regressors
Also, used 3dTproject to detrend PC regressors for appropriate censoring.
23 Sep 2016, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -select_runs option
16 Sep 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -radial_correlate option, to run @radial_correlate in proc script
14 Sep 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-bmax_ref ...' option: if bref has b>0.
Won't have much effective change *yet*, but will later. Possibly.
13 Sep 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
New opt -bref_mean_top to average over mean bref when b>0.
Also, totally reprogrammed most of interior; had been too scraggly.
31 Aug 2016, P Taylor, 3dSpaceTimeCorr, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug in yet-unreleased function... and also changed a feature.
Bug: ts = all0 -> GSL badness on some comp; now, exclude seedvox in corr.
31 Aug 2016, P Taylor, 3dSpaceTimeCorr, level 3 (MAJOR), type 1 (NEW_PROG)
New function for calculating spatial corr of temporal corr maps.
Calc spatial corr of WB/mask connectivity maps; useful for RSFC?
30 Aug 2016, RW Cox, 3dClustSimX, level 4 (SUPER), type 1 (NEW_PROG)
Generalized cluster simulation
Hopefully, the new way forward. Not ready for general users yet, but
getting there.
30 Aug 2016, RW Cox, 3dtoXdataset, level 2 (MINOR), type 1 (NEW_PROG)
Convert 3D datasets to a list of in-mask shorts
Purpose = compression for use in 3dClustSimX simulations. The '.sdat'
format is now directly write-able from 3dttest++, so this program is
probably not generally useful.
25 Aug 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix output.proc prefix in case -script has a path
Also, allow -mask_apply group in the case of -tlrc_NL_warped_dsets.
Thanks to C Capistrano and P Kim for noting the output.proc problem.
Thanks to C Connolly for noting the mask problem.
23 Aug 2016, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT)
add -fix_rich_quotes; if fixing a script, convert rich quotes to ASCII
Done for G Chen.
22 Aug 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
save all '3dAllineate -allcostX' anat/EPI costs to out.allcostX.txt
This is another quality control measure.
19 Aug 2016, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
can use surf_mask to restrict surface clustering
Use '-uvar surf_mask' to restrict on_surface clustering to mask.
Append SSCS command to end of script and handle NIFTI surf_vol.
The surf_mask mas added for C Thomas.
19 Aug 2016, DR Glen, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX)
Neighborhoods miscalculated
18 Aug 2016, P Taylor, 3dReHo, level 2 (MINOR), type 4 (BUG_FIX)
Used to not allow subbrik selection on input.
Now it does. Thanks to Daniel H. for pointing it out.
16 Aug 2016, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for new ACF/FWHM blur estimates
15 Aug 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
default clustsim method is now mixed model ACF
This marks afni_proc.py version 5.00.
o run 3dFWHMx with -ACF
o ACF and ClustSim files go into sub-directories, files_ACF/ClustSim
o -regress_run_clustsim now prefers arguments, ACF, FWHM, both, no
o default clustsim method is now ACF (via -regress_run_clustsim yes)
09 Aug 2016, DR Glen, @SUMA_MakeSpecFS, level 2 (MINOR), type 5 (MODIFY)
Atlasize original unranked datasets too. They will have more reliable indices than the ranked
05 Aug 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -marry_AM
Added for J Wiggins.
01 Aug 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
do more hunting and reporting on libgomp and libglib
01 Aug 2016, P Taylor, 3dRSFC, level 2 (MINOR), type 4 (BUG_FIX)
In cases of *very large* N_pts, an error message appeared-- no more.
Just changed default initialization of >f_N value.
11 Jul 2016, DR Glen, 3dWarp tta2mni grid dimensions bug, level 2 (MINOR), type 4 (BUG_FIX)
Ignored grid dimensions in transformation between Talairach to MNI
08 Jul 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE)
Extend -clustsim option
Covariates and centering
1- and 2-sided
unpooled and paired
1 sample as well as 2 sample
08 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -read_all, in case it is useful for sorting (e.g. -order_as_zt)
Added for K Vishwanath.
07 Jul 2016, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -order_as_zt to re-order from -time:tz to -time:zt
30 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow single volume EPI input (e.g. to test blip correction)
Also, auto -blip_forward_dset should come from tcat output.
30 Jun 2016, DR Glen, unWarpEPI.py anat to epi lpc+ZZ cost, level 2 (MINOR), type 4 (BUG_FIX)
Mistakenly used lpa for anat to epi alignment
29 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
can modify blip order; BLIP_BASE -> MEDIAN_BLIP; add BLIP_NOTE to help
29 Jun 2016, DR Glen, align_epi_anat.py flipping identity, level 2 (MINOR), type 4 (BUG_FIX)
Case of mistaken IDENTITY for check_flip option
24 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -requires_afni_hist; warp vr_base to make final_epi dset
22 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
do nothing, but work really hard at it
Rewrite EPI transformation steps by storing and applying an array
of transformations: this should make future changes easier.
21 Jun 2016, P Taylor, @fat_tract_colorize, level 3 (MAJOR), type 1 (NEW_PROG)
New function for coloring the volumetric tracking outputs.
RGB coloration of local diffusion, esp. for PROB track output.
20 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 4 (BUG_FIX)
Fixing bug in delta F calculation.
What more needs to be said?
16 Jun 2016, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 6 (ENHANCE)
EPI blip up/blip down distortion correction is ready
Thanks to S Torrisi and D Glen.
16 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if NLwarp but no EPI warp, no NL; fix refit of blip median datasets
User probably forgot -volreg_tlrc_warp, so warn them.
16 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 5 (MODIFY)
Changed how number of output points/freqs is calc'ed.
Should be more stable across group.).
14 Jun 2016, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Option -FWHMdset allows specifying per-voxel blurring parameter
For use with 3dLocalACF and scripting. EXPERIMENTAL!
14 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -blip_forward_dset; if needed copy along any obliquity information
14 Jun 2016, P Taylor, 3dAmptoRSFC, level 3 (MAJOR), type 1 (NEW_PROG)
New function for calculating RSFC params from one-side spectra.
Complements 3dLombScargle. What an epithet.
14 Jun 2016, P Taylor, 3dLombScargle, level 2 (MINOR), type 5 (MODIFY)
Making this output 'one-sided' spectra now.
Easier for 3dAmpToRSFC calcs.
13 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -align_unifize_epi : 3dUnifize EPI before anat alignment
Thanks to D Glen and S Torrisi for suggesting it.
13 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add BLIP_BASE case for -volreg_align_to
Use warped median forward blip volume as volreg alignment base.
13 Jun 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- AGAIN**2!-- now has Welch windows+tapers.
Scaling properly/consistently, couple bug fixes.
13 Jun 2016, DR Glen, 3dTstat - single sub-bricks, level 2 (MINOR), type 2 (NEW_OPT)
For datasets with only a single sub-brick, 3dTstat would exit
with an error for many statistics. The new behavior makes the
program use the first value of the time series instead. Some other
requested statistics like the argmax type stats are now calculated
even for this trivial case. Optionally the user may use
-firstvalue for a statistic
10 Jun 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -blip_reverse_dset for blip up/blip down distortion correction
09 Jun 2016, RW Cox, 3dLocalACF, level 2 (MINOR), type 1 (NEW_PROG)
Estimate ACF parameters locally. Slow and experimental.
09 Jun 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- AGAIN-- now has Welch windows+tapers.
Several new options added (related to windows/tapers).
03 Jun 2016, DR Glen, 3dQwarp bug, level 2 (MINOR), type 4 (BUG_FIX)
bug fix in option processing
Fixed wtprefix handling and gridlist option handling (with RCR)
02 Jun 2016, RW Cox, afni GUI, level 2 (MINOR), type 6 (ENHANCE)
Creation of All_Datasets session
If more than one session is input or created, then the All_Datasets
session is created as the catenation of all of them. This will help
people who want to look at data in multiple directories without moving
them together.
02 Jun 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
w/dglen: read num slices from Siemens 3D acquisition DICOM image files
27 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-scale_out_1000' option: rescale output, if desired.
Effectively: change output diff units of mm^2/s -> x10^{-3} mm^2/s.
24 May 2016, RW Cox, 3dUnifize, level 2 (MINOR), type 5 (MODIFY)
Alter default -clfrac value to 0.2
Because old 0.1 default would often have too much noise outside the head
when used with non-skull-stripped datasets. User can still set '-clfrac
0.1' if needed.
24 May 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 5 (MODIFY)
Revamped LS program-- new implementation, directly from PR89.
Several new options added (normalize, amplitudeize, etc.).
23 May 2016, RC Reynolds, parse_fs_lt_log.py, level 2 (MINOR), type 1 (NEW_PROG)
get an index list from a FreeSurfer labletable log file
20 May 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
add options -dot_file_list/_pack/_show
List, package (tgz) or show the contents of found 'dot' files.
19 May 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
-wball = emphasize some (spherical) region in the weighting
Written in Hangzhou China -- for Peng
16 May 2016, DR Glen, align_epi_anat.py - left/right test, level 2 (MINOR), type 2 (NEW_OPT)
left/right checking using align_epi_anat.py
flipped datasets go unnoticed even in major publicly available
databases (initially noted by Brad Buchsbaum with FCON1000).
Now automatically determine mismatch in L/R with simple test
New -check_flip and -flip_giant options check alignment against
flipped data.
12 May 2016, P Taylor, 3dLombScargle, level 3 (MAJOR), type 1 (NEW_PROG)
New function for calculating LS (normalized) periodogram from time series.
Calculate magnitude spectrum from non-equisampled data.
03 May 2016, P Taylor, @GradFlipTest, level 2 (MINOR), type 5 (MODIFY)
Using '-out_grad_cols_bwt' for grad stuff now-- use weights.
Can deal well with multiple DW factors in gradient list now.
02 May 2016, P Taylor, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Have a new '-min_bad_md' option: use to threshold badness.
Also now detect bad DT fits if MD is crazy big. Whoa.
28 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add -local_package, to use an already downloaded package
Requested by P Taylor.
27 Apr 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
prep for later: always extract volreg base, as vr_base*
19 Apr 2016, DR Glen, unWarpEPI.py, level 2 (MINOR), type 1 (NEW_PROG)
blip-up/down distortion correction script
08 Apr 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
auto-tcat inputs with spaces, wildcards and global selectors
For example, input of 'DA*.HEAD DB*.HEAD DC*.HEAD[3,4]' would create
a dataset with sub-bricks 3 and 4 from all D[ABC]*.HEAD datasets.
If sub-brick selectors appear only at the end, they are global,
otherwise they can be per input, as in 'DA*.HEAD[0,1] DB*.HEAD[2,3]'.
08 Apr 2016, P Taylor, 3dDTtoDWI, level 2 (MINOR), type 5 (MODIFY)
Work to deal with bvalue-weighted grads.
This is useful esp. for new TORTOISE outputs.
07 Apr 2016, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
add options -proto and -test_proto
One can specify the download protocol as http, https or NONE.
05 Apr 2016, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
fix bug with -5final -- but still hide from user
05 Apr 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
THD_open_tcat works as wildcard - can apply sub-brick selectors
05 Apr 2016, P Taylor, 3dDWUncert, level 2 (MINOR), type 2 (NEW_OPT)
New inp format option-- for dealing with TORT export/import.
-bmatrix_Z for reading in bmat in AFNI format; byebye -bmatr opt.
05 Apr 2016, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
New I/O options-- for dealing with TORT export.
Now have I/O of grad columns weighted by bvalues.
04 Apr 2016, RC Reynolds, THD_load_tcat, level 2 (MINOR), type 4 (BUG_FIX)
set factors and labels at open time, not at load time
This fixes use with 3dcalc and 3dinfo, though stats are not yet loaded.
25 Mar 2016, RW Cox, afni GUI, level 2 (MINOR), type 2 (NEW_OPT)
A bunch of '-XXX' options to control colors and fonts
22 Mar 2016, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
modularize version checking
Update .afni.vctime even if URL read fails, to not flood server.
17 Mar 2016, RW Cox, 3dTproject, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem in setting count of bandpass regressors
Typo meant that Nyquist frequency might not be counted properly,
resulting in bad stuff (memory corruption).
07 Mar 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed edge option change using too small neighborhood size
01 Mar 2016, RC Reynolds, tokens, level 2 (MINOR), type 1 (NEW_PROG)
program to extract valid text entries from a file
24 Feb 2016, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
replace tlrc_no_ss with anat_has_skull toggle and move to anat block
24 Feb 2016, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -warn_tr_stats crash on empty timing file
Thanks to Z Reagh for noting the problem.
19 Feb 2016, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
add many tests and summarize potential issues
11 Feb 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT)
-clustsim option
This option runs 3dttest++ with -randomize and then 3dClustSim with
-inset, to produce cluster-threshold tables for inclusion in the output.
It is my intention that this method will replace the use of 3dFWHMx and
3dClustSim. Knock wood, and help Make AFNI Great Again!
05 Feb 2016, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT)
New -inset option
Directly give the simulations, rather than generate them internally.
Intended for use with '3dttest++ -randomsign N -toz' and '3dttest++
-resid' to get the cluster thresholds directly from the data rather than
assumptions of Gaussianity.
27 Jan 2016, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow for tissue based regression with only regress block
26 Jan 2016, RW Cox, 1dNLfit, level 2 (MINOR), type 1 (NEW_PROG)
1D file nonlinear fitting
Uses the 'calc' parser to define the function to fit.
Mostly for the convenience of The Bob.
22 Jan 2016, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
rigid_body alignment option and better handling of user allineate options
05 Jan 2016, P Taylor, 3dVecRGB_to_HSL, level 3 (MAJOR), type 1 (NEW_PROG)
Take a 3-vec to a single index on RGB color scale, and glue FA brick.
Replaces earlier version, 3dVec_to_RGBind.
04 Jan 2016, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
add boundardy checks in get_1dcat_intlist and get_count_intlist
Without the checks, using count or 1dcat as sub-brick selector method
would lead to confusing crashes (if values exceeded #vols).
Thanks to W Graves for reporting the problem.
30 Dec 2015, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 2 (NEW_OPT)
add -acf option, to estimate FWHM via the ACF method
30 Dec 2015, RC Reynolds, afni-general, level 3 (MAJOR), type 6 (ENHANCE)
w/DRG implement new version system
See https://afni.nimh.nih.gov/pub/dist/MOTD/MOTD_2015_12_30.txt .
16 Dec 2015, P Taylor, 3ddot_beta, level 3 (MAJOR), type 1 (NEW_PROG)
Copy calc of 3ddot-- uses same functions-- just faster.
Right now, can only calculate eta2; was asked for by user.
08 Dec 2015, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY)
Add Write button to save just one cluster to a dataset
07 Dec 2015, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add -resid option, to save residuals.
01 Dec 2015, RW Cox, 3dClustSim, level 3 (MAJOR), type 2 (NEW_OPT)
Added -acf option!
Non-Gaussian spherically symmetric AutoCorrelation Function (ACF) for
the noise. Uses FFTs to create the noise fields, via #include-d file
mri_radial_random_field.c and #include-d csfft_OMP.c (thread-safe FFTs).
This method in 3dFWHMx and 3dClustSim will be the favored cluster
thresholding analysis going forward.
16 Nov 2015, P Taylor, 3dTrackID, level 3 (MAJOR), type 0 (GENERAL)
Estimate mean and stdev of fiber lengths in bundles.
These are now automatically output in *.grid file.
16 Nov 2015, P Taylor, 3dTrackID, level 3 (MAJOR), type 2 (NEW_OPT)
Can limit tracts to 'between targets' in new ways.
See '-targ_surf_stop' and '-targ_surf_twixt' in the help.
16 Nov 2015, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 5 (MODIFY)
New default for x-axis labels: rot=45 deg, horiz align=right.
Better than previous defaults (rot=37 deg, horiz align=center).
10 Nov 2015, RW Cox, 3dFWHMx, level 3 (MAJOR), type 2 (NEW_OPT)
-ACF option to compute spatial autocorrelation function
For enhancing 3dClustSim, et cetera.
10 Nov 2015, P Taylor, 3dVec_to_RGBind.c, level 3 (MAJOR), type 1 (NEW_PROG)
Take a 3-vec to a single index on RGB color scale, and glue FA brick.
This will be useful in prob tract result plotting... script to come.
28 Oct 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
output anat/EPI Dice coefficient, rather than correlation
28 Oct 2015, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
add -dodice, to get the Dice coefficient
26 Oct 2015, RW Cox, afni Clusterize, level 3 (MAJOR), type 6 (ENHANCE)
Allow user to use multiple (up to 4) Aux datasets for Plot/Save
26 Oct 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
compute TSNR restricted to uncensored TRs
28 Sep 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Use list of ROIs to select subnetwork of analysis for 3dMVM.
Previously, sublist only applied to post hocs, not 3dMVM models.
18 Sep 2015, DR Glen, @DBSproc bug fix, level 2 (MINOR), type 4 (BUG_FIX)
Left-right coordinate flip in @DBSproc script for Silvina Horovitz
16 Sep 2015, P Taylor, @GradFlipTest, level 3 (MAJOR), type 1 (NEW_PROG)
For DWI analysis: test whether grads need to be flipped.
Use a few tracking calls to estimate 'best' grad orientations.
01 Sep 2015, DR Glen, 3dcalc extreme, absextreme, level 2 (MINOR), type 2 (NEW_OPT)
New extreme and absextreme operators to find extreme values
21 Aug 2015, RC Reynolds, cifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
initial release: updated help and added -hist
New program to evaluate CIFTI datasets.
20 Aug 2015, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_isi_pdf and -show_isi_f_pdf
19 Aug 2015, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_missing, to show all missing labels from all files
12 Aug 2015, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
allow for generic/unknown commands via -command (e.g. ls, 3dTcat)
Done for W-L Tseng.
11 Aug 2015, RW Cox, 3dFWHMx, level 2 (MINOR), type 2 (NEW_OPT)
-1difMOD option
Computes the moments of the 1st differences, then estimates the mean and
standard deviation of the smoothness factors, then reports the mean
smoothness adjusted upwards to allow for the fact that 3dClustSim
depends more strongly on bigger smoothness than on smaller smoothness.
For use with single subject tests; probably too conservative for group
analyses.
10 Aug 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 2 (NEW_OPT)
Minor new option: input list of ROIs with file.
For minor convenience.
09 Aug 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when GM map has no ROIs/clusters.
No more crashing... Won't produce GM or GMI volumes; message only.
05 Aug 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
if conversion to NIFTI-1 header fails on write, try NIFTI-2
03 Aug 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added DTYPE_3DTM (3D+timing) ACQUSITION_TYPE
Treats data as per volume, but with slice timing. This is needed for
num_chan>0, but when data does not come in num_chan slices at a time.
29 Jul 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
ANATICOR now works with task analysis, using -regress_reml_exec
Done for R W Cox.
28 Jul 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
ANATICOR now includes zero volumes at censor points
This matches non-ANATICOR and fast ANATICOR cases.
27 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-dsort_nods option
When used with -dsort, this option will make 3dREMLfit calculate the
results with the -dsort regressors(s) omitted as well as the results
with the -dsort regressor(s) included -- so the user can compare the
dsort and non-dsort results easily with 1 run of the program. 'nods' ==
'no dsort'. Each nods dataset will have the string '_nods' appended to
the prefix.
23 Jul 2015, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -dsort option
Allows the addition of voxel-wise baseline regressors. To test out
ANATICOR applied to task-based FMRI data, for example.
22 Jul 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed minor bug when refset has negative values.
No more crashing...
17 Jul 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
Dimon->afni: small TCP buffers cause volumes to be passed slowly
In iochan_recvall, increase nap time only if packets < 4K are received.
13 Jul 2015, RC Reynolds, nifti_tool, level 3 (MAJOR), type 6 (ENHANCE)
nifti_tool is now based on NIFTI-2, with many corresponding new options
The old nifti_tool (based on NIFTI-1) is now nifti1_tool.
13 Jul 2015, RC Reynolds, NIFTI-2, level 3 (MAJOR), type 6 (ENHANCE)
added NIFTI-2 support into AFNI
Main source update: nifti/nifti2 tree, then applied it in mostly
thd_niftiread/write.c (plus gifti_io.h, 3ddata.h, mrilib.h).
To compile into all of AFNI edit: Makefile.INCLUDE, SUMA_Makefile_NoDev,
Makefile.avovk.INCLUDE and Makefile.ptaylor.INCLUDE.
13 Jul 2015, RC Reynolds, nifti1_tool, level 2 (MINOR), type 1 (NEW_PROG)
nifti1_tool is the NIFTI-1 version of nifti_tool
07 Jul 2015, P Taylor, fat_mat_sel.py, level 2 (MINOR), type 2 (NEW_OPT)
Simple new option to exclude x-axis labels.
They might just be annoying.
01 Jul 2015, RC Reynolds, cifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
reorg and more recur functions
24 Jun 2015, RC Reynolds, afni_xml_tool, level 2 (MINOR), type 2 (NEW_OPT)
afni_xml updates, and start to afni_xml_tool
18 Jun 2015, RC Reynolds, 3dExtrema, level 2 (MINOR), type 2 (NEW_OPT)
added -nbest
Output -nbest extrema; -quiet does not suppress extrema output.
17 Jun 2015, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added functions for reading from a buffer
16 Jun 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
applied -regress_stim_times_offset to typical timing files
Allows for stim timing offset when copying to stimuli directory.
16 Jun 2015, RC Reynolds, CIFTI, level 2 (MINOR), type 0 (GENERAL)
added initial nifti/cifti tree
15 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_cext
10 Jun 2015, RC Reynolds, @diff.tree, level 3 (MAJOR), type 1 (NEW_PROG)
look for differences between files in two directories
Should merge @diff.files and @diff.tree, and change to python.
10 Jun 2015, RC Reynolds, @diff.files, level 3 (MAJOR), type 1 (NEW_PROG)
compare list of files with those in other directory
01 Jun 2015, RC Reynolds, nifti_tool, level 2 (MINOR), type 6 (ENHANCE)
diff/disp_hdr detects type; diff_hdr1/2
26 May 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE)
nifti_read_header returns generic pointer; rename N-1/2 header read funcs
22 May 2015, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
allow for small differences when comparing oblique angles
Define OBLIQ_ANGLE_THRESH=0.01 as a tolerance for the difference.
This was done to fix registration to external dset in realtime.
Thanks to V Roopchansingh for bringing up the problem.
22 May 2015, DR Glen, 3dLocalstat mode, level 2 (MINOR), type 2 (NEW_OPT)
Find mode and non-zero mode in voxel neighborhood
21 May 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Minor bug fixed for inputting sublist of ROIs.
Short option for doing so worked, but not the long one; fixed now.
18 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow ROI PC regression for local masks (not just external ones)
External ROIs should now be passed via -anat_follower_ROI, rather than
-regress_ROI_*, the latter no longer taking dataset parameters.
Also changed -regress_ROI_erode to -anat_follower_erode and
removed option -regress_ROI_maskave (use -regress_ROI)
Done for R W Cox.
15 May 2015, P Taylor, 1dDW_Grad_o_Mat, level 2 (MINOR), type 2 (NEW_OPT)
Can output separate bval file.
Useful in some TORT preprocessing.
12 May 2015, RW Cox, 3dClustSim, level 2 (MINOR), type 5 (MODIFY)
Eliminate edge effects of smoothing by padding and unpadding
Simulate extra-size volumes then smooth, then cut back to the desired
volume size. Can use new '-nopad' option to try the old-fashioned
method. (H/T to Anders Eklund and Tom Nichols.)
08 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_make_corr_vols
Use this to compute average correlation volumes for various masks.
07 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
replaced slow 3dTfitter with 3dTproject in anaticor
This should not affect the result, just the processing time.
05 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added help (inc Ex 11), follower modifications, WMe corr diag change
04 May 2015, RW Cox, GLTsymtest, level 2 (MINOR), type 1 (NEW_PROG)
For testing symbolic GLTs in a script
So that the big boy (3dDeconvolve) doesn't have to be run just for this
purpose. To help out with afni_proc.py
04 May 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -anat_follower, -anat_follower_ROI, -regress_anaticor_label
29 Apr 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 5 (MODIFY)
allow reading and writing unknown extensions
28 Apr 2015, RC Reynolds, NIFTI, level 3 (MAJOR), type 6 (ENHANCE)
apply updates to NIFTI-2 I/O library
Also, include initial mods to nifti_tool, hidden under nifti2 dir.
28 Apr 2015, RC Reynolds, clib_02.nifti2, level 2 (MINOR), type 1 (NEW_PROG)
added clib_02.nifti2.c demo and Makefile under nifti2 dir
28 Apr 2015, RC Reynolds, NIFTI, level 2 (MINOR), type 0 (GENERAL)
add nifti/nifti2 directory with current NIFTI-1 versions of 4 files
This tracks initial changes to nifti2_io.[ch] nifti_tool.[ch].
27 Apr 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed output when byte/short insets were used.
Had been not writing data; needed to null brick_facs in outsets.
22 Apr 2015, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
add fix for non-unix files; allow for multiple tests with -prefix
22 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
put in cat_matvec string to create warp.all.anat.aff12.1D
Thanks to sgreen (MB) for noting the problem.
22 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add -todo; help update; verify use of erode list
15 Apr 2015, ZS Saad, suma-general, level 3 (MAJOR), type 4 (BUG_FIX)
Turned off USE_XOR for now.
Was causing very mysterious problem with labels displaying atop each other
in the SUMA viewer. Possibly other problems too like crash when opening
surface controller or changing threshold. No time to get to the bottom
of this at this time. But turning this off fixed problem on linux and osx.
Valgrind had nothing to complain about...
08 Apr 2015, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
updated to Ziad's new -revert option
03 Apr 2015, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Changes to how labeled datasets (volumes in particular) are shown in SUMA
Made atlas and labeled volumes appear in SUMA as they do in AFNI.
No labels show up upon clicking though. Appearance of labeled dataset
will change for labeled datasets created earlier, unless env.
SUMA_Classic_Label_Colors is set to YES
02 Apr 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -tlrc_NL_warped_dsets to import 3dQwarp result
Added for P Molfese and others.
01 Apr 2015, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
anat followers and ROI_PC
Datasets can follow the anatomical warps
Added options -regress_ROI_PC, -regress_ROI_maskave, -regress_ROI_erode.
PC allows for some number of principle components to be regressed, and
maskave is for mask averages to be regressed.
The _erode option applies to either, and happens before xform.
Also, any anat with skull is applied as a follower.
Also, -tcat_remove_first_trs can now take a list.
30 Mar 2015, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update for selenium
Includes: Makefile.linux_openmp*, xorg7*, osx_10.7*, fedora19_64,
as well as Makefile.INCLUDE and rickr/Makefile for LLIBS.
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Selection now possible on VR rendered image in SUMA
27 Mar 2015, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed syntax for env SUMA_VO_InitSlices, space chars are bad.
27 Mar 2015, DR Glen, Selenium webdriver to open webpages, level 3 (MAJOR), type 0 (GENERAL)
Opens webpages without multiple tabs using python selenium webdriver
23 Mar 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 4 (BUG_FIX)
Fixed projection error in SUMA_NN_GeomSmooth?_SO
23 Mar 2015, RW Cox, 3dttest++, level 3 (MAJOR), type 2 (NEW_OPT)
Add -singletonA option
For testing one subject vs a collection of 'normals'. Works with
covariates.
23 Mar 2015, RC Reynolds, python-general, level 2 (MINOR), type 6 (ENHANCE)
broke VarsObject class out into separate file
19 Mar 2015, RC Reynolds, unix_tutorial, level 2 (MINOR), type 6 (ENHANCE)
populated AFNI_data6/unix_tutorial with Sphinx version
The previous tutorial was moved under 'old'.
18 Mar 2015, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Node depths were being computed along the principal direction closest to Z
The proper intent is along the principal direction, regardless of
whether or not it is closest to the Z direction
18 Mar 2015, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added -node_depth
18 Mar 2015, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added options -in_range, -ex_range for thresholding and output COM and Cent
These changes resulted in numerous small changes throughout the code for
a more uniform handling of thresholding methods
18 Mar 2015, RC Reynolds, sphinx, level 3 (MAJOR), type 6 (ENHANCE)
added unix_tutorial to the doc tree
13 Mar 2015, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Added ExistsAs in ParseName
This can find whether or not you have datasets on disk with some
view (+tlrc), say given only a prefix.
13 Mar 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added code to receive and store ECHO_TIMES
This is passed as control information and is stored in rtin->TE.
13 Mar 2015, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added V Roopchansingh update for T2* est Merge function
12 Mar 2015, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -pc* and -key options to compute coordinate PC of clusters.
See -help for details.
11 Mar 2015, ZS Saad, 3dSeg, level 3 (MAJOR), type 2 (NEW_OPT)
Added -mixfloor to avoid getting NAN when certain classes disappear.
Also added -mixfrac IGNORE to turn off any modulation by the mixing
fraction during the EM routines.
11 Mar 2015, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
added covary and linear_fit; -listfunc takes -/stdin to read from stdin
04 Mar 2015, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Added WHelp button to mimic BHelp but open online pages
This required a few additional modifications to the auto-help
generating functions. Lots of work under the hood.
03 Mar 2015, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed misuse of strncat in distribution
26 Feb 2015, ZS Saad, IsoSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -autocrop and -mergerois+dset
See help for details
26 Feb 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 2 (NEW_OPT)
Added -no_zero_attraction
See help for details
26 Feb 2015, DR Glen, align_epi_anat.py align_centers bug, level 2 (MINOR), type 4 (BUG_FIX)
align_centers always called by mistake
25 Feb 2015, ZS Saad, IsoSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -remesh option to simplify meshes
24 Feb 2015, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 6 (ENHANCE)
re-wrote method: new decon, upsample, multiple files, reconvolve
This is partially for evaluation of the decon/recon PPI steps.
23 Feb 2015, ZS Saad, suma-general, level 3 (MAJOR), type 5 (MODIFY)
Allow SUMA to break a surface into multiple drawing patches
This makes it possible to show certain parts of a mesh based on
a nodemask. The nodemask can be generated on the fly and updated with
mouse clicks. This is only available in -dev mode. See SUMA_DrawMesh_mask(
)
and temporary env SUMA_TEMP_NODE_CMASK_EXPR
23 Feb 2015, ZS Saad, IsoSurface, level 3 (MAJOR), type 2 (NEW_OPT)
Made IsoSurface handle ROI volumes better
See options -mergerois, -isorois for details
23 Feb 2015, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Set transparency and rendering modes per object
See ctrl+o, ctrl+p
19 Feb 2015, DR Glen, @Align_Centers child bug, level 2 (MINOR), type 4 (BUG_FIX)
child datasets not created properly
If creating new shift datasets (the default), the
datasets would not be properly updated to reflect
the new origin shift.
17 Feb 2015, DR Glen, align_epi_anat.py center alignment, level 2 (MINOR), type 2 (NEW_OPT)
-ginormous_move and -align_centers added
Added call to @Align_Centers for initial center alignment
The -align_centers option can be used by itself with the
transformation matrix included in the combination transformation.
Adding the center alignment on to giant_move, given the nom
of ginormous_move. Note these options ignore any obliquity
in the original datasets.
12 Feb 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_anaticor_fast/-regress_anaticor_fwhm
This implements the 'fast' ANATICOR method, computing the WMeLocal
voxel-wise regressors via an FWHM Gaussian sum of WMe voxels, rather
than a uniform sum within a radius.
10 Feb 2015, RW Cox, afni GUI, level 2 (MINOR), type 0 (GENERAL)
Ability to graph time series with x-axis from another dataset
Voxel-by-voxel x-axis selection. Previously (Jan 1998) could only do
x-axis as a 1D file == fixed for all sub-graphs. Now each voxel can get
its own x-axis. God help you.
09 Feb 2015, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
warn on '\' without preceding space
Gang and J Rajendra ran into a problem on OS X 10.9.5.
09 Feb 2015, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
applied updates matching 3dClustSim (9 table output)
Output from 3dClustSim is now 9 tables: NN=1,2,3 by 1-,2-,bi-sided tests.
09 Feb 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Can threshold bundles with too few tracks; TRK files not default out.
Useful to control false pos; useful to save space outputting.
05 Feb 2015, RW Cox, AFNI InstaCorr, level 2 (MINOR), type 0 (GENERAL)
Add Iterate option
03 Feb 2015, RC Reynolds, model_conv_PRF, level 2 (MINOR), type 6 (ENHANCE)
consolidate blur and reorg into one function, to reduce max memory usage
This allows the program to run on weaker systems, cutting the max RAM
usage by one half. A prior step was to allocate main RAM early so that
free() would release to the OS (Linux), but that is now moot.
This change has no effect on the results (no binary diff).
02 Feb 2015, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Take coords from a surface rather than just a file for -com node_xyz
30 Jan 2015, ZS Saad, BrainSkin, level 2 (MINOR), type 2 (NEW_OPT)
Added -vol_skin and -vol_hull to create smooth contours of mask volume.
30 Jan 2015, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT)
Improvements to SOLID fill method and addition of option -ed
30 Jan 2015, RW Cox, Clusterize, level 2 (MINOR), type 0 (GENERAL)
Add Bi-sided clustering
Goes along with the new 3dClustSim, which now generates tables for that
case as well. 'Bi-sided' means positive above-threshold voxels are
clustered separately from negative below-minus-threshold voxels. Note
that bi-sided is turned off for 1-sided thresholding and/or Pos func,
even if the user turns bi-sided on in the Clusterize chooser.
29 Jan 2015, RW Cox, afni GUI, level 3 (MAJOR), type 0 (GENERAL)
Use new 3dClustSim tables
Now Clusterize chooses the table to use based on the threshold type (t-
or F-stat, say), and if 1-sided thresholding was chosen by the user.
Also, the p-value below the slider now adjusts if the user chose to do
1-sided thresholding on a 2-sided statistic (t-stat, correlation,
z-score).
29 Jan 2015, RW Cox, 3dClustSim, level 3 (MAJOR), type 0 (GENERAL)
Compute NN=1,2,3 and 1-sided, 2-sided, bi-sided tables
In sum, all 9 tables are ALWAYS computed now.
27 Jan 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 5 (MODIFY)
Include main effects of interaction vars in post hoc tests.
Hadn't been testing these previously.
26 Jan 2015, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 4 (BUG_FIX)
Hadn't included part quantitative interaction term in qVars list.
Program wouldn't run if interaction term had quant var.
26 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Can dump output *maps*, not just masks, of each connection.
See '-dump_rois AFNI_MAP' for how it works.
23 Jan 2015, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Added -stat list and -stat hist* .
23 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Rare scenario of -nifti -dump_rois AFNI not working.
Needed to add a mkdir() internally. Itsafinenow.
23 Jan 2015, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
Web-based links in Whereami GUI on by default
Links will be available by default now. Effectively
equivalent to setting these environment variables to YES:
AFNI_WEBBY_WAMI, AFNI_SUMSDB and AFNI_NEUROSYNTH.
22 Jan 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fixed some issues when only a tiny number of voxels is in inset.
Labelling wasn't correct when nvox < n_refset_roi.
20 Jan 2015, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
SumsDB link
Link out from whereami GUI in afni to SumsDB database
with new environment variable AFNI_SUMSDB (YES/NO).
Must also set AFNI_WEBBY_WAMI to YES.
14 Jan 2015, RC Reynolds, read_matlab_files.py, level 2 (MINOR), type 1 (NEW_PROG)
read and possibly convert MATLAB files to 1D format
09 Jan 2015, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Released new documentation to the wild.
09 Jan 2015, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Made sure neighborhoods containing central voxel return its value 1st.
09 Jan 2015, ZS Saad, 3dLocalstat, level 2 (MINOR), type 5 (MODIFY)
Added -*diffs options for computing local differences
07 Jan 2015, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
Add -gridlist and -allsave options
Allows specifying the exact list of patch/grid sizes to use, and also to
save the output warp at each level.
07 Jan 2015, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Switch to output nifti files.
For PAIRMAP, INDIMAP and -dump_rois output.
07 Jan 2015, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT)
Switch to output nifti files.
For GM and GMI files.
07 Jan 2015, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
Switch to output nifti files.
For corr map or Z map files.
29 Dec 2014, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Lot of additions to SphinxDocs/SUMA, plus auto-doc for SUMA controller
22 Dec 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added All Objs button to initialize controllers for all objects if desired
21 Dec 2014, P Taylor, fat_mat_sel.py, level 4 (SUPER), type 1 (NEW_PROG)
Plot, view and save matrix file info.
Works for both 3dNetCorr and 3dTrackID info.
21 Dec 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 0 (GENERAL)
Change of string output in .niml.dset.
Make the label match the ROI string labels.
21 Dec 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 0 (GENERAL)
Output NIML dset automatically.
This allows users to view connectivity matrix info in SUMA easily.
18 Dec 2014, DR Glen, VmPFC atlas, level 2 (MINOR), type 0 (GENERAL)
Ventro-medial prefrontal cortex atlas
Worked with Scott Mackey to make maximum probability map atlas available
15 Dec 2014, P Taylor, 3dROIMaker, level 3 (MAJOR), type 2 (NEW_OPT)
Make a subset of an ROI by choosing maximal neighboring values.
Start with peak value, add neighboring max until N voxels selected.
10 Dec 2014, ZS Saad, imcat, level 2 (MINOR), type 2 (NEW_OPT)
Added -autocrop* options
09 Dec 2014, RW Cox, afni GUI, level 2 (MINOR), type 5 (MODIFY)
Add 'Alpha' fading to overlay
In this mode, the outlines of the supra-threshold regions are outlined
(unless AFNI_EDGIZE_OVERLAY is NO). Alpha fading is turned off in
Clusterize at this time, since it would be complicated to make the 2
things work together.
05 Dec 2014, RW Cox, 3dNwarpApply, level 3 (MAJOR), type 4 (BUG_FIX)
Forgot to index-ize the matrix warps before applying them!
In the revised way of catenating time-dependent warps, the matrix warps
are kept in xyz coords until they are actually used, when they should be
transformed to ijk coords. In the 'old' way, they were transformed
directly on input. But in the 'new' way, I forgot to transform them
before applying them in the catenation loop, and the results were not
pretty. I'm still searching for someone to blame for this, since it
clearly can't be MY fault. Any volunteers?
04 Dec 2014, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Added -handedness option.
04 Dec 2014, DR Glen, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT)
1Dmat_only_nodset option
Undid former fix because other scripts may rely on these shifted datasets
and added new option. Datasets will not be output or modified with
new option, and just the transformation matrix is output
02 Dec 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
added floatscan to THD_load_nifti for case of double->float conversion
Thanks to M Gregory.
02 Dec 2014, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
fixes for child_anat and mean epi base
Thanks to Isaac Schwabacher for the child_anat fix!
01 Dec 2014, RW Cox, 3dNwarpApply, level 3 (MAJOR), type 0 (GENERAL)
Extensive changes to make operations more general
(1) Allow catenation of warps with different grid spacings -- the new
Nwarp_catlist struct and functions will re-grid to make them match.
(2) Allow input of affine warps with multiple time points, so that
3D+time datasets can be warped with a time dependent Nwarp_catlist.
(3) Allow input of multiple source datasets, so that several datasets
can be warped the same way at once. This is more efficient, since the
auto-catenation in the Nwarp_catlist will only have to be done once.
(3a) Specification of the output dataset names can be done via multiple
arguments to the '-prefix' option, or via the new '-suffix' option.
26 Nov 2014, ZS Saad, 3danisosmooth, level 2 (MINOR), type 2 (NEW_OPT)
Output of diffusion measures, along with adjustment of debug volumes
For details, see tersely named option -save_temp_with_diff_measures,
along with modified help for -savetempdata
24 Nov 2014, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Fixed clash between matrix.h and matrix_f.h
Clash was my own doing, I had introduced it by including matrix.h
via suma_string_utils.h into 3ddata.h. The conflict has been resolved
now. Care must be taken to include matrix_f.h early in a .c file and
that would stop the inclusion of matrix.h from suma_*.h files.
24 Nov 2014, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 4 (BUG_FIX)
Fixed floating point precision error that resulted in error message
21 Nov 2014, ZS Saad, afni-general, level 3 (MAJOR), type 5 (MODIFY)
More and more and more changes to the -help
Devised system to simplify, so to speak, the generation of
sphinxized help. Changes span multiple functions, most visible
are the sphinx_printf() and its siblings, and new options in apsearch.
See program 3dToyProg.c for an example on how to write help for C programs
.
See also Writing_Help.rst for more details.
18 Nov 2014, RW Cox, 3dTRfix, level 2 (MINOR), type 1 (NEW_PROG)
Interpolate from a variable TR grid to a fixed TR grid
For Javier et alii. No T1 artifact correction, just interpolation.
11 Nov 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
GraphCont->CN->Col now abide by the 'u' selection for unconnected nodes
11 Nov 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Made matrix display labels track selection
09 Nov 2014, DR Glen, whereami connections, level 2 (MINOR), type 5 (MODIFY)
Web display includes connections links
Developed for macaque connection webpages
07 Nov 2014, RC Reynolds, model_conv_PRF_6, level 2 (MINOR), type 1 (NEW_PROG)
6 parameter population receptive field estimate model
Added sigrat (sigma ratio) and theta parameters.
For E Silson and C Baker.
05 Nov 2014, P Taylor, 3dROIMaker, level 3 (MAJOR), type 3 (NEW_ENV)
Default neighborhoods now AFNI standard; labeltable functionality in.
Default 'hoods more standard, can still do other; labels by default.
05 Nov 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Switch to not output INDI and PAIR map files.
In connectome examples, this might save a lot of space.
04 Nov 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Continued modifications for help generating functions, now with selfies
Now SUMA can take selfies of the varied widget frames, making the
documentation easier to generate. This involved adding a new version
of ISQ_snapfile() called ISQ_snapfile2() and a rendering of a colormap
in X11. Search for Fake_Cmap for relevant locations in C code.
03 Nov 2014, G Chen, rPkgsInstall, level 2 (MINOR), type 1 (NEW_PROG)
Install/check/update/remove R packages on the terminal
This is an R program that allows the user to install,
check, update, or remove R packages on the shell terminal.
27 Oct 2014, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added 107 face images for 20 years
27 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed strcmp trap in -sbns; have -sb_num_suffix look for any last integer
24 Oct 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 4 (BUG_FIX)
Fixed offset in track to volume coordinates
Effect of bug restricted to viewing of tracts rather than volume masks and
connectivity matrices.
Offset was by half a voxel in each of the three dims.
23 Oct 2014, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
enhanced read_text_file and added shuffle_blocks
22 Oct 2014, RW Cox, 3dNwarpApply, level 3 (MAJOR), type 5 (MODIFY)
Alter -nwarp option a lot
Specifically, allow time-dependent matrix inputs in any position in the
-nwarp catenation stream (only for this program, not the fixed-warp
programs 3dNwarpCat, 3dNwarpXYZ, 3dNwarpFuncs). Removes the -affter
option, which is now absorbed into the -nwarp processing.
20 Oct 2014, RC Reynolds, imcat, level 2 (MINOR), type 4 (BUG_FIX)
z and r: fixed y-padding
20 Oct 2014, DR Glen, Haskins Pediatric templates and atlases, level 3 (MAJOR), type 0 (GENERAL)
Nonlinear and affine versions of Haskins Pediatric templates and atlases
New templates with matching segmentation atlases are provided for
pediatric subjects, ages 8-12
17 Oct 2014, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Modifications for help generating functions
New tools allow for automatic Sphinx formatted documentation straight
from BHelp buttons. Added scrolling to arrow fields.
17 Oct 2014, ZS Saad, afni-general, level 3 (MAJOR), type 0 (GENERAL)
Checked in first pass of SUMA sphinx documentation
GUI documentation is automatically generated from BHelp text.
17 Oct 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -load_masks, -save_masks, and -masks for driving tract controller
Options help in creating all GUI help and herald the automation of the
tract and tract masking controller.
16 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added sort_methods: none, acq_time, default, num_suffix, zposn
15 Oct 2014, ZS Saad, imcat, level 2 (MINOR), type 2 (NEW_OPT)
Added -respad_in, -gscale, and -pad_val options
Process involved modifications to mri_read_resamp_many_files(),
mri_zeropad_2D(), and a new mri_valpad_2D(). See imcat -help for details.
10 Oct 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added directions and point clouds as DOs
See interactive help for #directions, #points
08 Oct 2014, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
added -save_errors and more recovery chances, fixed sb_num_suffix app
Stage 3 of sorting broke stage 2 of sorting.
Thanks to V Roopchansingh for noting the problem.
07 Oct 2014, ZS Saad, AFNIio.R, level 2 (MINOR), type 2 (NEW_OPT)
Allowed specification and inheritance of TR in write functions
07 Oct 2014, RW Cox, InstaCorr in AFNI GUI, level 2 (MINOR), type 5 (MODIFY)
Multiple sections to be correlated
Input 'Start,End' in the format 'Start@Length,Number,Delta' to get
sections of the given 'Length'.
30 Sep 2014, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug with NUMLOCK keeping surfaces from rotating on linux!
26 Sep 2014, P Taylor, 3dTrackID, level 3 (MAJOR), type 2 (NEW_OPT)
Allow labeltable reading and writing.
This allows users to use labeltables, and output labelled values everywher
e.
26 Sep 2014, P Taylor, 3dNetCorr, level 3 (MAJOR), type 2 (NEW_OPT)
Allow labeltable reading and writing.
This allows users to use labeltables, and output labelled values everywher
e.
23 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Allowed interactive cluster thresholding by node number (-ve Area value)
Previously this was possible only via command line's -n option.
Command line now also supports negative -amm2 values if -n is not set.
23 Sep 2014, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added some explicit -help and improved the few existing options
23 Sep 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
cat_strings was missing trailing byte
Thanks to Q Li for noting the problem.
22 Sep 2014, ZS Saad, 3dGenFeatureDist, level 2 (MINOR), type 2 (NEW_OPT)
Added -hspec to explicitly set histogram generation parameters
22 Sep 2014, RC Reynolds, column_cat, level 2 (MINOR), type 4 (BUG_FIX)
fixed implementation of -line, which messed up default operation
19 Sep 2014, RC Reynolds, 3dexample1, level 2 (MINOR), type 1 (NEW_PROG)
sample program to multiply a dataset by 2
This is very basic example of reading/processing/writing AFNI datasets.
18 Sep 2014, P Taylor, fat_mvm_scripter.py, level 2 (MINOR), type 2 (NEW_OPT)
Allow interaction terms in the user-defined statistical model.
Allow cat+quant or cat+cat variable interactions, and posthoc testing.
17 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
A few miscellaneous errors here and there
One was caused by extra space in driver command
Another was caused by loading multiple surfs on the command line
followed by a command line drive command.
Intersection parameters were not fully initialized under some conditions.
17 Sep 2014, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -pc_proj and -node_depth options.
These options are meant to help localizing seeds along DBS electrodes.
Relevant C code functions: SUMA_NodeDepth(), SUMA_Project_Coords_PCA()
and SUMA_*_PC_XYZ_Proj()
17 Sep 2014, DR Glen, MNI nonlinear templates, level 2 (MINOR), type 5 (MODIFY)
Nonlinear version of MNI-152 template in distribution
The nonlinear 2009c version is more useful, particularly as a base for
nonlinear alignment. AFNI_atlas_spaces.niml includes descriptions for
native MNI152 2009c T1 template and a transformed version aligned to
the TT_N27 dataset in Talairach space
16 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Use of percentiles in range settings was broken. That is no more.
Problem was caused by reliance on colp->V without resetting it
when a new range was set. That is because colp->V gets clamped
by the range of values being set.
16 Sep 2014, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -fill_dirs option, to specify directions for hole filling
Added for D. Glen.
15 Sep 2014, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
apply -prefix for -show_file_type (a dos2unix conversion)
12 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Crosshair mismatch when prying surfs in multiple linked viewers
12 Sep 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash caused by toggling off 'I' selection for volumes
08 Sep 2014, P Taylor, fat_roi_row.py, level 4 (SUPER), type 1 (NEW_PROG)
Select out one row of a matrix file, at user request.
Useful, for example, if wanting to view connectivity one-to-many.
08 Sep 2014, P Taylor, fat_mvm_scripter.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- write a basic command call to 3dMVM.
User specifies specific model, and awaaaay we go.
08 Sep 2014, P Taylor, fat_mvm_prep.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- combine CSV and matrix data.
Build data table necessary for 3dMVM from MRI+other data.
08 Sep 2014, P Taylor, fat_mvm_gridconv.py, level 4 (SUPER), type 1 (NEW_PROG)
Connect FATCAT with 3dMVM-- modernize format of old *.grid files.
Prehistoric grid files had no labels. This updates them.
08 Sep 2014, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT)
Allow pre-inflation of an input ROI, at user request.
Useful, for example, if wanting to go from WM->GM.
04 Sep 2014, DR Glen, AFNI_ATLAS_PATH, level 2 (MINOR), type 3 (NEW_ENV)
Atlases and templates may be stored in location set by AFNI_ATLAS_PATH
Atlases and templates need not be in the default afni binary directory.
This variable may hold multiple directories that specify the possible
locations of atlases when the atlas definition does not include the
path in the filename. The atlases are typically defined in
AFNI_atlas_spaces.niml file or in a CustomAtlases.niml file
03 Sep 2014, ZS Saad, 3dSetupGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Made -labels option work well with -LRpairs
03 Sep 2014, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
merged in changes from C Craddock, with alterations
This needs some more work.
29 Aug 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added -drive_com to allow the driving of SUMA by its command line
28 Aug 2014, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT)
Added -equalized to do histogram equalization on the whole volume
25 Aug 2014, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Added -*PrefixView, and improved -out to multi-components
25 Aug 2014, ZS Saad, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
Made program handle NIFTI input. Irrrrgh.
22 Aug 2014, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sort_method and -save_details
Using the 'geme_index' sort method allows for real-time sorting
of GE multi-echo data, before volumes are sent to 'afni'.
Modification made for V Roopchansingh.
12 Aug 2014, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
this should basically work like the old version
While no major change should be seen, this is an overhaul of
the previous version, which should allow for realtime sorting.
12 Aug 2014, RC Reynolds, Dimon1, level 2 (MINOR), type 0 (GENERAL)
Dimon1 is a fork of the previous working version of Dimon
This can be a backup if there are troubles with the new Dimon.
05 Aug 2014, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Made program handle FreeSurfer's -contrasurfreg output
05 Aug 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 5 (MODIFY)
Less memory usage and a bit faster.
More efficient internal handling of quantities.
04 Aug 2014, P Taylor, 1dDW_Grad_o_Mat, level 3 (MAJOR), type 2 (NEW_OPT)
Can edit dataset with averaging B0s and DWIs.
Should make life easier for dual processing of vecs and datasets.
04 Aug 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
New option for PAIRMAP labelling by X, not 2^X; new *.grid NT scaling.
Make PAIRMAP easier to view; user wanted extra matrices.
02 Aug 2014, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT)
added -run_trs, for cases when the TRs per run vary
Requested on message board by Rebecca and later by Lisam.
01 Aug 2014, ZS Saad, 3dGenFeatureDist, level 2 (MINOR), type 1 (NEW_PROG)
Program written a while ago, placed in the distribution now
15 Jul 2014, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
output average motion per stim over response
This will probably be replaced by averages over stimulus only time.
Requested by D Pine.
11 Jul 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed 1d_tool.py -pad_into_many_runs for bpass w/varying run lengths
Thanks to d6anders for noting the problem.
09 Jul 2014, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Mean b=0 values computed for linear estimate
New -mean_b0 option allows for averaging of b=0 values
used in linear model and initial linear estimate for nonlinear
method.
03 Jul 2014, RC Reynolds, model_conv_PRF, level 2 (MINOR), type 4 (BUG_FIX)
fixed a name space problem on macs
03 Jul 2014, DR Glen, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
oblique NIFTI dataset handling
NIFTI datasets with oblique orientations were written
with incorrect (original) orientations after alignment. Dataset is
now cardinalized and input obliquity is ignored
02 Jul 2014, RW Cox, 3dNwarpXYZ, level 2 (MINOR), type 1 (NEW_PROG)
Nonlinear transform of xyz coordinate triples -- for Ziad
30 Jun 2014, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
Add -lpc and -lpa options
Sounds simple, but was really a lot of work to make these reasonably
efficient. And to work at all, for that matter. Ugh.
27 Jun 2014, RC Reynolds, model_conv_PRF, level 3 (MAJOR), type 1 (NEW_PROG)
population receptive field estimate model
For E Silson and C Baker.
26 Jun 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
full_mask is now byte (via 3dmask_tool); note correlation with anat mask
26 Jun 2014, RC Reynolds, 3dresample, level 2 (MINOR), type 2 (NEW_OPT)
added -bound_type FOV/SLAB option (FOV is orig and default)
FOV preserves the field of view, SLAB preserves the SLAB
(so with SLAB the extents should not change)
25 Jun 2014, RC Reynolds, to3d, level 2 (MINOR), type 6 (ENHANCE)
allow -zorigin with x/y SLAB/FOV, particularly in case of nz==1
25 Jun 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
removed SUMA/SUMA_MakeColorMap, SUMA/SUMA_MakeConsistent from source tree
Thanks to Y Halchenko for bringing it up.
19 Jun 2014, RW Cox, @Install_ClustScat_Demo, level 2 (MINOR), type 1 (NEW_PROG)
Installs demo for Clusterize scatter plotting
19 Jun 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
Added new feature: output partial correlation matrices.
Can output r-like and beta-like partial correlation matrices.
18 Jun 2014, RW Cox, afni GUI, level 2 (MINOR), type 5 (MODIFY)
Move Clusterize outside of Instastuff menu
So Clusterize is now available for InstaCorr, etc. The bkgd:xxxx box is
gone, its functionality living on only in the 'u' image keypress.
13 Jun 2014, DR Glen, afni, level 2 (MINOR), type 0 (GENERAL)
Jump to MNI or any space coordinates
Jump to MNI in afni GUI enhanced to recognize current dataset
space and not assume MNI to TLRC transformation. Also can jump
to other space coordinates by setting AFNI_JUMPTO_SPACE in
.afnirc or Environment plugin
07 Jun 2014, ZS Saad, auto_warp, level 2 (MINOR), type 2 (NEW_OPT)
Made -dataTable options take text file instead of command line opts
This makes it possible to have very large tables without exceeding
limit on command line length. File name has to begin with '@'
in keeping with some C-language 3d progs.
06 Jun 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 0 (GENERAL)
Changed how it runs, mainly under the hood; added '-thru_mask' option.
Cleared some old arrays; make runable as function; user wanted thru_masks.
03 Jun 2014, RW Cox, afni GUI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_PBAR_FULLRANGE
If this variable is set to YES, then the color pbar in Define Overlay
will reflect the range set by the user for the colorization process. At
some point, this feature will become the default, and then you'll have
to set this variable to NO to get the old behavior -- where the range
set by the user is shown only at the bottom right of the Define Overlay
panel, and it then multiplies the independently set top value of the
pbar to get the colorization scale. In the new method, the top value of
the pbar cannot be set by the user independently of the range (or
autorange) parameter. The intention of this change is to make the
number -> colors process somewhat more blatant.
02 Jun 2014, ZS Saad, auto_warp, level 2 (MINOR), type 2 (NEW_OPT)
Added -qworkhard and -qw_opts for finer control of 3dQwarp step
30 May 2014, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
if PREFIX ends in .nii, all saved datasets will be in NIFTI format
Added for V Roopchansingh.
23 May 2014, DR Glen, whereami linkrbrain, level 2 (MINOR), type 4 (BUG_FIX)
Fixed linkrbrain coordinates and malloc/free error
Coordinates were not transformed properly from TLRC to MNI
space. Crashes from clusterize in afni GUI caused by mismatched
AFNI-friendly malloc, free in strdup function
21 May 2014, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Option -iname to give filename as appearing on the command line
20 May 2014, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
macs: look for PyQt4 from homebrew and fink
16 May 2014, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
a few updates:
- if no AFNI binaries in path, try path to ASC.py
- look for history files in data directories
- print comments at end, so they are easier to notice
16 May 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
changed default of -anat_unif_GM to no
Use of -GM in 3dUnifiize was leading to some skull stripping failures.
Thanks to J Stoddard for noting the problem.
16 May 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
make space in case compression programs have longer paths
Thanks to D Thompson for finding the problematic code.
13 May 2014, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
allow for no stats dset
With resting state and 3dTproject, afni_proc.py will not create stats.
12 May 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_use_tproject, and made the default=yes
This will apply 3dTproject instead of 3dDeconvolve for resting
state analysis. It is much faster, and creates the same result.
05 May 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_HomeAfterPrying to avoid a 'home' reset with prying
02 May 2014, DR Glen, align_epi_anat.py, level 2 (MINOR), type 0 (GENERAL)
NIFTI dataset input
align_epi_anat.py modified to allow NIFTI input for anat,epi,
child_epi datasets. Output continues to be AFNI format.
01 May 2014, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
added -quick option; fixed recursive backups
29 Apr 2014, P Taylor, 3dROIMaker, level 2 (MINOR), type 2 (NEW_OPT)
Freedom in neighbor defs; also can keep just N peak values per ROI.
User can specify face, edge or vertex ngbs. Also, search for N max vals.
29 Apr 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
Added new feature: output WB correlations as Zscores.
Can output WB maps of ROI average time series correlations as Z-scores.
24 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Reading of OBJ file format for triangular meshes.
24 Apr 2014, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -multi_timing_to_event_list
This allows one to generate simple or details event lists, or to
partition one event class by its predecessors.
Partitioning added for W Tseng.
21 Apr 2014, P Taylor, TORTOISEtoHere, level 4 (SUPER), type 1 (NEW_PROG)
New program: convert TORTOISE DTs to AFNI format.
This also allows flipping/rescaling to be done.
21 Apr 2014, P Taylor, 3dEigsToDT, level 4 (SUPER), type 1 (NEW_PROG)
New program: take in eigen{values,vectors} and calculate DT.
This also allows flipping/rescaling to be done.
21 Apr 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 2 (NEW_OPT)
Added new feature: do whole brain correlations.
Can output individual WB maps of ROI average time series correlations.
18 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Allow graph dataset bundle references to be located based on gdset's path
This way if a graph dataset named GDSET refers to a tract file TRACT
using a relative path (./TRACT) and you use suma -gdset SOMEPATH/GDSET
to load the graph, then the search for TRACT will also consider SOMEPATH/
as an option
18 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Color map changes/thresholding changes now working with multi-viewers
This was not the case before. Problem was that Texture had to be reloaded
for all viewers displaying the volume, once the viewer's rendering context
is current. That's all handled via per_sv_extra[]
17 Apr 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -controller_position to position object controller window
16 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with opening new controllers when cont. window is closed
See Apr. 16 2014 note in function SUMA_viewSurfaceCont()
16 Apr 2014, ZS Saad, 3dTcorr1D, level 2 (MINOR), type 5 (MODIFY)
Turned heart of main() into a standalone function in thd_Tcorr1D.c
This way we can run the equivalent of 3dTcorr1D from other C programs
such as 3dNetCorr
16 Apr 2014, ZS Saad, 3dRprogDemo, level 2 (MINOR), type 1 (NEW_PROG)
A toy program to show how to write a command line R program with AFNI
Created to help Cesar Caballero and Natalia Petridou implement their
Paradigm Free Mapping method.
16 Apr 2014, RW Cox, 3dNwarpAdjust, level 2 (MINOR), type 0 (GENERAL)
Changes for grid size requirements
Now the warps don't all have to be on the same grid (just conformant
grids), and they will be extended to match each other. And the source
datasets (if present) don't have to be on the same grid as the warps,
but DO have to be on the same grid as each other -- as before.
16 Apr 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added MIN_OUTLIER parameter option for -volreg_base_dset
Using '-volreg_base_dset MIN_OUTLIER' will result in the volume with
the minimum outlier fraction to be extracted as the volreg base.
Thanks to T Ross for the good suggestion, so long ago
16 Apr 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 5 (MODIFY)
Reformatted output a bit, added features for J. Rajendra.
Can output time series with labels, and as individual files.
16 Apr 2014, P Taylor, 3dMatch, level 2 (MINOR), type 4 (BUG_FIX)
Bug when using mask on *some* files with Linux.
Seems to be more stable criteria now.
15 Apr 2014, RW Cox, 3dQwarp, level 2 (MINOR), type 0 (GENERAL)
and other warping functions
Changes to index warps, to extend them past their defining box by linear
extrapolation from the last 5 layers on each face (vs. the previous
method of just constant extrapolation). Also use this in 3dNwarpApply
to extend the warp before using it, so as to deal with peculiar results
with non-padded inverse warps from 3dQwarp when there was a big
displacement via '-allin'. Speaking of which, I also extended the
zero-padding in 3dQwarp to allow for the large displacements. By
default, WARP outputs from 3dQwarp are not truncated any more, but can
be with the new '-nopadWARP' option. Next up -- changes to
@toMNI_Qwarpar to allow for collections of warps that may be on
different grids.
15 Apr 2014, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
added optional 'pid' parameter to the get_process_stack() functions
10 Apr 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
@afni.run.me never made it into Makefile.INCLUDE for distribution
10 Apr 2014, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -index_to_run_tr, intended for use by afni_proc.py
09 Apr 2014, RC Reynolds, gen_ss_review_table.py, level 3 (MAJOR), type 1 (NEW_PROG)
parse output from @ss_review_basic text into spreadsheet format
This makes it easy to flag outlier subject values.
Thanks to J Jarcho for encouragement.
09 Apr 2014, DR Glen, whereami supplemental web-based info, level 2 (MINOR), type 0 (GENERAL)
Atlases may have supplemental information available from a website
Further information can be opened through a web browser for individual
structures. This feature is implemented initially for the support of the
Saleem macaque atlas.
08 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'F10' to toggle prying axis between Z and Y
08 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_VO_InitSlices controls how volumes slices are shown at startup
See ~/.sumarc for details, run suma -update_env if variable is missing.
08 Apr 2014, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Draw mask surface sent from SUMA, for delectation.
Add a SUMA_mask struct type to afni_suma.h, and then process its
corresponding NIML element in afni_niml.c. Masks are stored in the
THD_session struct, and are re-drawn when their center is altered by a
simple command (unlike normal surfaces). Also changed -- always send
change of crosshairs to SUMA even if no surfaces are present -- let SUMA
figure out what to do with it (e.g., move the mask).
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Made prying do both hinge rotation and translation
Difference is in the direction of mouse motion.
Also made vertical prying cause rotation about screen x axis for spheres
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_Dset_NodeConnections controls how connections to a node are displayed
See ~/.sumarc for details, run suma -update_env if variable is missing.
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added three modes for controlling how connections to a node are shown.
This makes it possible to greatly reduce the clutter of the display.
See menu 'CN' that controls this
04 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
A double select click makes all graph edges appear.
This only has an effect if the current object in focus is a
graph object
04 Apr 2014, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed reading NIFTI obliquity w/dglen (lost Mar 22)
Thanks to P Kundu for noting the problem.
04 Apr 2014, DR Glen, whereami -linkrbrain, level 2 (MINOR), type 2 (NEW_OPT)
New option for getting task or gene correlation with coordinate list
Linkrbrain.org support is available in alpha form from whereami and
the Clusterize GUI. AFNI_LINKRBRAIN needs to be set to YES to use new
features.
03 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_Dset_Font to initialize text in graph datasets
See ~/.sumarc for details, run suma -update_env if variable is missing.
02 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Made AFNI's crosshair changes move tract mask in SUMA
This happens when the viewer is in Mask Manipulation Mode.
02 Apr 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Made SUMA_crosshair_xyz carry information on overlay dataset
This is in response to a request by Nick Oosterhoff
31 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -anat_unif_GM (def=yes); improved message for bad ricor input
28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'F11' to allow users to set the object rendering order
This is an interactive version of env: SUMA_ObjectDisplayOrder
28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Implemented doppleganger for masks on pried surfaces
28 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added prying along the horizontal direction too
This is most handy when you want to travel along the
lateral surface and still see what gives in tracts or on
slices.
26 Mar 2014, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Wrote a new function to handle input events
New function SUMA_RecordEvent() records X events into a structure
that I can clone and attach into the Pick Results struct. Without
this, I can't tell down the line if a pick was with shift+control
or without it. A problem when deciding what to tell AFNI, for example
The new functions (see also SUMA_ShftCont_Event() and other functions
around it should replace all queries in SUMA_input() about event
qualifiers. Still need to check about handling of button swap, or
conditions when drawing, etc.
26 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Made double-click right click outside of objects turn off mask movement
26 Mar 2014, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
Shift+Control+right click in SUMA will trigger Instacorr refresh in AFNI
This way you can click on an object in SUMA and still get AFNI to
so a volumetric ICOR computation, with all accompnaying talk back to SUMA.
etc.
26 Mar 2014, RC Reynolds, auto_warp.py, level 2 (MINOR), type 4 (BUG_FIX)
in 3dNwarpApply, use the base dataset as the -master, rather than WARP
The WARP dataset is now often bigger, to handle warps to the dataset
edges. The result from auto_warp.py should match the template/base.
Note: the problem applies to binaries from 3/21 until 3/25 (now).
Thanks to V Zachariou for noting the problem.
25 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -anat_uniform_method and -anat_opts_unif
This correction may be particularly useful along with either
-tlrc_NL_warp or -mask_segment_anat.
24 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_anaticor_radius
This specifies the radius for the local white matter average.
Option requested by S Torrisi.
21 Mar 2014, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
added -data_root and enhancements for class data search
21 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if anaticor and censor, do not use keep_trs for blur est from errts
Thanks to J Stoddard for noting the problem.
20 Mar 2014, RC Reynolds, 1dUpsample, level 2 (MINOR), type 4 (BUG_FIX)
fix reporting of file name in error messages; enhance said messages
18 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Improved selection logic on slices and for graphs.
Graph selection was changed so that what is rendered is selectable.
The alternate was too confusing.
Fixed bug with selections on matrix where selections at times were
going to the volume, even though it is not displayed with the matrix.
Fixed slice highlighting when in montage mode.
Added alpha value threshold condition to slice picking. This slows the
selection process a little, but it keeps one from selecting 'air' when
when clicking on voxels that meet the threshold but are alpha masked.
17 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed residual surface shading after volume is selected.
Problem was caused by residual emissivitiy colored left over
from the highlighting of the selected slice. Also wrote functions
SUMA_DiffEnablingState*() to help identify such problems.
14 Mar 2014, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
added some data and OS-specific tests
13 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
More improvements to multiple object transparency.
There's lots more than meets the eye. See comment in functions
SUMA_DrawVolumeDO_3D() and SUMA_StippleMask_shift()
13 Mar 2014, ZS Saad, afni_open, level 2 (MINOR), type 2 (NEW_OPT)
A few more tweaks, like -aw and -d
See afni_open -help for details
12 Mar 2014, ZS Saad, afni_open, level 2 (MINOR), type 1 (NEW_PROG)
A simple program to help us open certain files on typical machines
There is no help for the program yet, it is also not part of the
compiled binaries yet. New functions such as GetAfniWebDownloader(),
GetAfniPDFViewer(), and GetAfniImageViewer() were added to machdep.c
12 Mar 2014, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
set errts_pre in anaticor block; apply extends in blur no scale
06 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added option to make rendered slices jump to new cross hair location
See new function SUMA_VO_set_slices_XYZ() for details
06 Mar 2014, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
changed some censoring and per-stim behavior
- if censoring, create X.stim.xmat.1D from uncensored matrix
- if no censor, still report num regs of interest and TRs per stim
- report per-stim censoring only with stim classes
06 Mar 2014, P Taylor, 3dTrackID, level 5 (SUPERDUPER), type 5 (MODIFY)
Have Cordelialy unified the three kingdoms of tracking, cLearing usage.
This program does all tracking, including HARDI and mini-probabilistic.
06 Mar 2014, P Taylor, 3dProbTrackID, level 5 (SUPERDUPER), type 5 (MODIFY)
Put out to pasture.
This program is now retired, with usage cleanly transferred to 3dTrackID.
06 Mar 2014, P Taylor, 1dDW_Grad_o_Mat, level 3 (MAJOR), type 1 (NEW_PROG)
Manipulate gradient/bmatrix files.
Convert row/col and grad/bmatrix/gmatrix, use bval info, filter or not.
06 Mar 2014, P Taylor, 3dTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Changes for reading in DTI files.
Allow NIML-formatted input file, as well as globbing in ordinary case.
06 Mar 2014, P Taylor, 3dNetCorr, level 2 (MINOR), type 5 (MODIFY)
Reformatted output a bit.
Make output easier to read, labelled, and matching *GRID files.
06 Mar 2014, P Taylor, 3dDWUncert, level 2 (MINOR), type 2 (NEW_OPT)
Changes for reading in DTI files.
Allow NIML-formatted input file, as well as globbing in ordinary case.
06 Mar 2014, P Taylor, 3dDWUncert, level 2 (MINOR), type 4 (BUG_FIX)
Silly bug-- order of options not free.
Changed how options were processed so they weren't order-dependent.
05 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Fixed initial setting of masks to be relative to center of tracts object
This required creation of SUMA_ADO_Center() and SUMA_ADO_Range() functions
.
05 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Opening surf controller after selecting voxel on slice caused crash in demo
This happened in FATCAT_DEMO's Do_09* script, example 1 (SET1). While I am
still unsure what caused the Bad Window error, I now trap for it and keep
the program from getting shutdown. Some day I'll track the source of the
message, for now, recovery seems complete.
04 Mar 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Surface-based InstaCorr stopped refreshing with new click.
The problem was caused by the failure to update the copies of I and
T columns in the overlay structure when a new dataset replaced an older
version. For the fix, search for 'ResetOverlay_Vecs' string, and see
function SUMA_DSET_ClearOverlay_Vecs()
25 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added loading/saving of masks and evaluation expressions to GUI.
25 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added tract length masking in Masks GUI.
25 Feb 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
Added -dset_labels option to label dset sub-bricks.
Normally 3drefit would handle that, but not for graph dsets, not yet
at least
19 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash during crazy matrix rotations.
The problem was caused by divisions by very small sizes under certain
projection (viewing) angles
19 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed indexing errors in sparse matrices with certain node (point) lists.
The problem occurred when point lists were supersets of the points used to
define the edges.
19 Feb 2014, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -Clst and -UseClst options to DriveSuma
18 Feb 2014, ZS Saad, suma, level 3 (MAJOR), type 5 (MODIFY)
Added tract masking with boolean expressions
This allows users to specify the masking function
using the various masks as variables in a boolean expression.
The interface also allows for the coloring of various tracts based
on which masks they travel through. This addition is only available
with the -dev option, though the restriction will soon be lifted.
18 Feb 2014, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test_local_timing, to look for local vs. global timing issues
- in some cases, promote married types to combine/compare them
- keep track of '*' entries from timing files
10 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed ordering of objects displayed to prevent graph text masking
10 Feb 2014, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
show TRs per run, applied and censored
06 Feb 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Increased Maximum number of viewers to 10 for Javier's desire
To allow the increase without needlessly waisting memory,
the color lists now only created if a viewer is open.
That still means as many color lists for almost each type of data
carrying object. But the allocation is only done if the viewer is
open. Volume objects share the same color list and perhaps tracts
should do the same, in the future.
The downside of sharing is that coloration will
be the same across all viewers for the same object.
31 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with graph where segments were turning black.
Problem was caused by a stale pointer copy stored in SDO->colv
bad bad bad!
31 Jan 2014, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Lessened dependency on new libgsl to allow FATCAT build on xorg7
This necessitated creating a double version of thd_correlate()
and adding -DXORG7 to the xorg7 makefiles
31 Jan 2014, DR Glen, AFNI_IMAGE_GLOBALRANGE, level 2 (MINOR), type 3 (NEW_ENV)
New options for scaling display in afni GUI
AFNI_IMAGE_GLOBALRANGE can be set to SLICE (default), VOLUME (SUBBRICK),
or DSET. The GUI applies the lookup table to color the underlay with the
range determined from the slice, sub-brick or the whole multi-sub-brick
dataset. This environment variable may be set in a user's .afnirc file,
Additionally, the GUI allows changes from the environment plugin menu or
in two new places - the right-click menu on the image viewer colorbar.
Typing Control-m in an image viewer cycles among the global range types.
Previous YES/NO definitions for this variable correspond to VOLUME and
SLICE respectively and will continue to work as before. The lower right
corner of the image viewer shows the current range setting:
(2%-98%/Min2Max, Vol, Dset)
29 Jan 2014, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
-brickwise allows time-dependent t-test results
For Stephen Robinson
23 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Added transparency for slice displays
23 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Added GUI for tract mask editing
23 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Added volume rendering in addition to slice rendering
No clipping planes yet.
15 Jan 2014, RW Cox, afni image viewer, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_CROP_AUTOCENTER - automatically re-center crop sub-window
If set to YES, then the crop sub-window (if cropping is active) will
automatically re-center about the crosshair location -- as far as
possible. This feature can also be set for each image viewer window
separately from the intensity bar right-click popup menu. (NOW will
John Butman be happy?)
09 Jan 2014, DR Glen, 3dDWItoDT, level 2 (MINOR), type 4 (BUG_FIX)
bmatrix options
bmatrix_Z and bmatrix_NZ options replace old -bmatrix option
The new options allow for a B=0 and no B=0 row in an optional
b-matrix input. The b-matrix may be used as input instead of the
gradient vector direction file. The former -bmatrix option
resulted in an error or incorrect results. (Paul Taylor is mostly
responsible for recognizing and fixing this. Thanks, Paul!)
08 Jan 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
Added -graph_XYZ_LPI to flip coords to RAI for the user.
08 Jan 2014, ZS Saad, ConvertDset, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem introduced by earlier -graph_named_nodelist_txt change
Problem was one of parsing and made the program fail to read in all
entries in labels file.
06 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Set proper voxel identification in interface. No more resampling.
RAI resampling is no longer needed, but stil available by setting
SUMA_VO_Reorient.
03 Jan 2014, ZS Saad, suma, level 3 (MAJOR), type 5 (MODIFY)
Big improvements to slice rendering
Improvements include proper alpha masking and auto thresholding
Montage-like capability.
Percentile thresholding and intensity range setting
Fixed intersection bug with multi-slice rendering
03 Jan 2014, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Modernized some driver handling functions to use ADO instead of SO
Improvements will allow easier driving of SUMA for non-surface
objects. For now we're not quite there yet. Soon one hopes.
31 Dec 2013, ZS Saad, suma, level 3 (MAJOR), type 5 (MODIFY)
Improvements to tract rendering
Added stenciling to allow for rendering of masked tracts without
interfering with unmasked tracts
30 Dec 2013, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
for -show_bad_backslash, check for '\' as the last file character
The fix (with -prefix) is to delete the last '\' and end with a newline.
27 Dec 2013, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
also output censored TRs per run, along with fractions
27 Dec 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_tr_run_counts and -show_num_runs, for gen_ss_review_scripts.py
26 Dec 2013, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
max and jump to cluster max are now based on masked dset, if possible
24 Dec 2013, ZS Saad, InstaTract, level 2 (MINOR), type 1 (NEW_PROG)
Wrote the outlines of InstaTract to eventually perform miniprob tracking
The program now talks to SUMA and receives queries from it.
The queries return a dummy network for now. PT will make it interface
with FATCAT to compute the actual tracts.
23 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added option to hide graph nodes when nothing is connected to them
23 Dec 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for F12 key from DriveSuma
18 Dec 2013, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 5 (MODIFY)
if system files seem to exist in the abin directory, block update
If AFNI seems to be installed in a system directory (i.e. with OS level
programs), default to not letting the update proceed. Options -sys_ok
and -help_system_progs were added to provide control and details.
17 Dec 2013, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
SUMA stopped building on systems lacking glCheckFramebufferStatus()
That was basically all linux_* systems since they are quite a few
versions behind. The patch is activated with a define at make time.
Set SUMA_MDEFS = -DSUMA_GL_NO_CHECK_FRAME_BUFFER in Makefile.* if
the OpenGL installed does not support glCheckFramebufferStatus().
Note that -DSUMA_GL_NO_CHECK_FRAME_BUFFER is not really needed for
most build machines because the code uses other ways to check for
glCheckFramebufferStatus(). However these auto checks failed on
hurin so SUMA_GL_NO_CHECK_FRAME_BUFFER is still necessary for the moment
17 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Allowed graph node coloring based on a graph point's group ID
To use such a coloring scheme, set Cl --> Grp in the surface controller
for a graph dataset. To set group IDs and color, see ConvertDset's
option -graph_named_nodelist_txt
17 Dec 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
ConvertDset's -graph_named_nodelist_txt now takes node grouping and color
See -graph_named_nodelist_txt's help section for details
17 Dec 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
use -NEW by default with 3dDespike
Added -despike_new to override the default behavior.
16 Dec 2013, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed use of num_trs in the case of censoring
Thanks to K Kerr for noting the problem.
16 Dec 2013, RC Reynolds, auto_warp.py, level 2 (MINOR), type 2 (NEW_OPT)
added -qblur option for P Molfese
11 Dec 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Wildcard file expansion with extension and view trimming and sorting
See apsearch's -help output with all the -wild_* options for detail.
Functions at the heart of all this are unique_str() and MCW_wildcards().
11 Dec 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Added -afni_web_downloader
Done via GetAfniWebDownloader()
10 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Reduced memory load by about a factor of 5 when dealing with volumes
This was done by sharing color lists across viewers. This would be
appropriate when volumes are colored the same way across viewers, a
likely scenario. Further reductions can be made by going from
GLfloat * to GLbyte *, sometime in the future perhaps.
10 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed source of undefined buffer and problem with glXMakeCurrent on OS X
Problem seems caused by attempting to create an X graphics context when
creating a new suma viewer. XCreateGC is no longer needed - its context
has not been used for a long while anyway.
09 Dec 2013, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed broken demo script run_stdmesh_demo from std_meshes.tgz
Failure was in glXMakeCurrent which crashed rather than return in error.
Not sure what was causing this, but it was the rapid succession of
controllers being open and repositioned that was causing this. Simply
splitting the two operations into separate loops was enough to remedy
this. Adding calls to glFinish() and XSync() did nothing to fix the
problem reliably
09 Dec 2013, RC Reynolds, afni_util.py, level 2 (MINOR), type 4 (BUG_FIX)
added backup function for get_process_stack
BASE.shell_com() might return a short process list, probably from
limited buffer space (for cmd.stdout).
06 Dec 2013, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Automated decision for calling glXMakeCurrent with SUMA_glXMakeCurrent()
This fixes instances where surfaces were being rendered in the colorbar!Ev
entually any use of SUMA_Si_Si_I_Insist() should be obsolete.
04 Dec 2013, RC Reynolds, afni_runme, level 2 (MINOR), type 1 (NEW_PROG)
added this (Ziad's) script to sysadmin/scripts
04 Dec 2013, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
fixed ac++ condition and empty if
03 Dec 2013, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
added -prog_list for Ziad
29 Nov 2013, RW Cox, 3dDespike, level 2 (MINOR), type 2 (NEW_OPT)
add -NEW option
Different fitting method than L1 -- much faster, results not identical,
but does that matter for an ad hoc algorithm?
27 Nov 2013, ZS Saad, 3dCM, level 2 (MINOR), type 2 (NEW_OPT)
Added -roi_vals to get COM for multiple ROIs
Workhorse is THD_roi_cmass() in thd_center.c
04 Nov 2013, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Made functions transforming afni volumes to suma dsets preserve types
Formerly much was changed into floats. Affected functions include:
nsd_add_colms_type(), SUMA_afnidset2sumadset(), and nsd_add_sparse_data()
01 Nov 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
let all-1 input for extents mask vary per run (for diff # TRs)
31 Oct 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
restrict blur estimation to uncensored TRs
31 Oct 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_trs_run
This will be used by afni_proc.py to restrict TRs for blur estimation
to those that were not censored, per run.
30 Oct 2013, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Add 'blowup' to image viewer saver
From interactive dialog AND from SAVE_xxx driver commands.
30 Oct 2013, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
added -keep_dirent_pre, to expand subject ID to directory entry prefix
Requested by P Molfese.
28 Oct 2013, P Taylor, 3dROIMaker, level 2 (MINOR), type 5 (MODIFY)
Allow multiple-brick masks.
For N-brick data set, can input either 1- or N-brick mask.
28 Oct 2013, P Taylor, 3dMatch, level 2 (MINOR), type 4 (BUG_FIX)
Fixed subbrick labelling oddity.
For some reason, subbrick selection with [i] was getting confusedwith i-th
label (which was an integer). Solved by prefixing labeldesignation with a
short string of useful letters.
24 Oct 2013, P Taylor, 3dROIMaker, level 2 (MINOR), type 4 (BUG_FIX)
Fix segmentation error when not using -refset.
Fixed error in defining/freeing a certain array.
21 Oct 2013, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -xmulti option
For graphing with different x-values for different y-value 1D files.
21 Oct 2013, DR Glen, whereami GUI, level 2 (MINOR), type 3 (NEW_ENV)
NeuroSynth.org link
Link out from whereami GUI in afni to neurosynth.org
with new environment variable AFNI_NEUROSYNTH (YES/NO).
Must also set AFNI_WEBBY_WAMI to YES.
01 Oct 2013, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Made suma send filename of surface volume to AFNI
In this manner a -sv volume that is not in AFNI's
current session will still be loaded into the current session
See afni function AFNI_append_dset_to_session() and wherever it
is used for details
01 Oct 2013, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Made AFNI seek and add to session a missing SUMA surface volume
See afni function AFNI_append_dset_to_session() and wherever it
is used for details. That function is under afni_plugin.c which is one
of the few .c files with access to the GLOBAL_library structure.
01 Oct 2013, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Reduced AFNI complaints of missing surface volumes and extra triangles.
These messages come up for each surface component 'nel' and are highly
redundant. Now messages are choked to about once every 2 seconds for
each message id. See whine_about_idcode() for details.
30 Sep 2013, RC Reynolds, unix_tutorial, level 2 (MINOR), type 6 (ENHANCE)
updates to installs/unix_commands/scripts/basic_*/bin/*
These are for the 2 Dec 2013 bootcamp.
26 Sep 2013, P Taylor, TrackIO.c, level 2 (MINOR), type 5 (MODIFY)
Improving ease of track handling.
Updated TrackCreate function, which has simpler inputs from 3dProbTrackIDn
ow; outputs unchanged.
26 Sep 2013, P Taylor, DoTrackit.c, level 2 (MINOR), type 5 (MODIFY)
Improving ease of NOT-mask ROI inclusion and (internal) track handling.
This is useful/necessary for handling new NOT-mask regionality in networkf
iles for tracking; think it just streamlines various processing, as well.
26 Sep 2013, P Taylor, 3dROIMaker, level 2 (MINOR), type 5 (MODIFY)
Allow negative ROIs in refset.
This is useful/necessary for handling new NOT-mask regionality in networkf
iles for tracking.
26 Sep 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 5 (MODIFY)
Improving ease of NOT-mask ROI inclusion and (internal) track handling.
Instead of separate ROI NOT-masks, uses can build in ANTI-ROIs withnegativ
e-valued (=-1) voxels.Under the hood track handling: smoother checking of
track ends, as well asof possibly breaking up tracks in event of NOT regio
ns; simpler passingto track bundles, as well.
23 Sep 2013, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Numerous updates/bug fixes for graph dset handling
Pick buffer update now synced with what viewer shows.
See SUMA_ADO_Flush_Pick_Buffer(). Text, whenever displayed,
is turned into a solid rectangle in the pick buffer to facilitate
selection.
Point radius based on value was improperly scaled, same for stippling
Gain arrows had a min of 1.0, now min is 0 and max 200
Background of text now updates along with text color when color of viewer
background is changed.
Help message for picking updated.
Shift+Alt+Button-3 press will now take a snapshot of the pick buffer
to help with debugging.
19 Sep 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow regress_polort -1; added help for -regress_RSFC
19 Sep 2013, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
allow AFNI_COMPRESSOR to init decompression tool between gzip/pigz
19 Sep 2013, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
show label->sub-brick index conversion via AFNI_SHOW_LABEL_TO_INDEX
19 Sep 2013, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
added options -get_processed_env[_afni] and -global_opts
16 Sep 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Switched functions of mouse buttons 1 and 2 when viewing GRAPH MATRIX
This means matrix spatial rotation would be done with button 2 and
shifting with button 1. Selection can also be done with button 3 whenever
there is no selectable surface in sight.
16 Sep 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY)
Add zero-padding
To allow for images that run right up to the edge of the volume, where
displacements are defined to be zero, so those parts of the volume won't
be warped. Zero-padding extends the volume, which will avoid such
issues. It is turned on by default, and can be turned off by '-nopad'
(as in 3dAllineate).
12 Sep 2013, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Added possibility to store network tracts in external file for graph dsets
See 3dProbTrackID's -gdset_toy for an illustration.
Some small changes were made to ptaylor/ files to allow for this.
12 Sep 2013, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL)
added P Taylor's Makefile and install notes
Makefile.linux_ubuntu_12_64, OS_notes.linux_ubuntu_12_64
12 Sep 2013, RC Reynolds, afni-general, level 2 (MINOR), type 0 (GENERAL)
added afni_src/other_builds directory
This is for non-AFNI-build Makefiles and OS install notes.
It has been initialized with:
Makefile.linux_fedora_19_64
OS_notes.linux_fedora_19_64.txt
11 Sep 2013, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Small changes to make Yaroslav's Debian tests work better
Changes to @DO.examples to fit Debian installations
Changed SUMA_search_file to avoid searching entire path and
focus on AFNI specific regions instead.
Made DriveSuma's kill_suma command less onerous.
11 Sep 2013, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allow for surface specification with symbolic notation
Option -i now can parse strings like: ld60:MNI_N27:l:smoothwm
to load surfaces from template volumes that would be stored
in the afni data directory (see THD_datadir()).
Also the -spec option can now take such symbolic notation
11 Sep 2013, RC Reynolds, model_conv_cosine4, level 3 (MAJOR), type 1 (NEW_PROG)
A four half-cosine convolvable model.
Based on: Fully Bayesian Spatio-Temporal Modeling of FMRI Data
IEEE Transactions on Medical Imaging,
Volume 23, Issue 2, February 2004, Pages 213-231
Woolrich, M.W., Jenkinson, M., Brady, J.M., Smith, S.M.
Requested by C Connolly and Felix.
03 Sep 2013, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
Dimon -rt: if im_is_volume and single volume, get dz from image
Thanks to A Nilsen for reporting the problem.
26 Aug 2013, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Program crashes or gets bad answers on very large datasets
Problem: with a vectim, the pointer to the k-th voxel time series array
(of length nvals) is calculated as
ptr = base + k * nvals
where k and nvals are ints. But with gcc, the k*nvals value is then
computed in 32 bit arithmetic before being added to the 64 bit pointer
'base'. Not good when you pass the 2,147,483,647-th voxel -- that is,
if the vectim is over 8 Gbytes. With the Intel icc, it apparently works
OK -- bravo for Intel. Anyhoo, by casting k and nvals to size_t, this
problem goes away. For now.
26 Aug 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
added -check_all, -find_prog, -casematch, -exact
These changes are to add PATH searching for programs.
26 Aug 2013, P Taylor, DoTrackit.c, level 2 (MINOR), type 4 (BUG_FIX)
Fix handling of non-RPI datasets.
No ostensible output change, except to not produce an error message.
23 Aug 2013, RW Cox, 3dTproject, level 2 (MINOR), type 5 (MODIFY)
Add catenation, for RCR
21 Aug 2013, P Taylor, 3dProbTrackID, level 3 (MAJOR), type 5 (MODIFY)
Putting together old deterministic and probabilistic programs into 1.
Unifying tracking, will be easier to update/improve in future.For determin
istic tracking, allow networks of target ROIs for tracking,as well as bund
ling outputs for SUMA network/matrix viewing.New option as well, `-mini_pr
ob', to have some probabilistic aspect todeterministic/tract-based output.
21 Aug 2013, P Taylor, 3dTrackID, level 2 (MINOR), type 5 (MODIFY)
Minor changes in internal trackbundle handling/NIML-output.
Temporary step to SUMAfication of program; this program willeventually be
phased out in favor of 3dProbTrackID deterministic options.
21 Aug 2013, P Taylor, 3dRSFC, level 2 (MINOR), type 4 (BUG_FIX)
Allow subset of time series to be selected.
Minor tweaking of internal workings for writing output.
No quantitative change.
20 Aug 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_RSFS, to run 3dRSFC
Would run 3dRSFC per run on errts, to bandpass and compute parameters.
19 Aug 2013, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Dreaded __builtin_object_size came up for 3dTproject
Replace memcpy with AAmemcpy in cs_symeig.c . Separated OMP
macros from mrilib.h by putting them in Aomp.h
16 Aug 2013, ZS Saad, suma-general, level 3 (MAJOR), type 5 (MODIFY)
Yet another still hidden expansion of graph dsets
Modifications to many data structures and handling functions
to allow for the storage and display of graph datasets (such as
correlation matrices, and the like.
16 Aug 2013, ZS Saad, afni-general, level 3 (MAJOR), type 5 (MODIFY)
Changes to tractography I/O API to allow for graph dataset handling
Effort in concert with Paul Taylor
14 Aug 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
removed '_' from PYTHON_PATH; note any /sw/bin/python* files
14 Aug 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added non-linear standard space registration via -tlrc_NL_warp
09 Aug 2013, RW Cox, 3dTproject, level 2 (MINOR), type 1 (NEW_PROG)
Rapid orthogonal projection to remove unwanted time series
To replace 3dBandpass when necessary
06 Aug 2013, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Recreated suma_MNI_N27.tgz and suma_TT_N27.tgz with LPI GIFTI
The surfaces had to be recreated to fit LPI assumption.
Old suma will not work with new archives and vice versa.
SUMA will warn when using old archive to help users with transition
See @SUMA_Make_Spec_FS -nocor and -GNIFTI options for more info.
06 Aug 2013, ZS Saad, MapIcosahedron, level 2 (MINOR), type 5 (MODIFY)
Hard coded skipping of outer-pial-smoothed surfaces
Those brain envelopes are not isotopic with the rest of
the surfaces so there is no point standardizing them.
05 Aug 2013, ZS Saad, inspec, level 2 (MINOR), type 2 (NEW_OPT)
Added -remove_state to remove surfaces of specific state from spec file
05 Aug 2013, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY)
Option -nocor is now obsolete. -GNIFTI replaces it
This was necessary to alert whoever was using -nocor that
resultant GIFTI surfaces were being written in RAI and that now
they are in LPI in keeping with the standard.
See @SUMA_Make_Spec_FS -nocor and -GNIFTI options for more info.
02 Aug 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
check for multiple R and python programs in PATH
02 Aug 2013, RC Reynolds, 3dANOVA, level 2 (MINOR), type 4 (BUG_FIX)
if AFNI_COMPRESSOR and input nii.gz, 'remove()' would not remove BRIK.gz
Thanks to P Molfese for noting the problem.
01 Aug 2013, RC Reynolds, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
in suma_gifti.c, convert GIFTI's LPI to and from AFNI's RAI
Done with Ziad. Thanks to N Oosterhof for bringing this up.
01 Aug 2013, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fixed apparent pointer step issue, which happens on only some systems
Apparent problem with MMAP (memory mapping of files).
Thanks to W Gaggl for pointing out the problem.
31 Jul 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -xmat_1D NegXY to flip X Y coordinate sign of surfaces.
This should make it easy to turn GIFTI files with RAI units to
LPI with something like:
ConvertSurface -i toy.gii -o_gii toy -overwrite -xmat_1D NegXY
31 Jul 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -merge_surfs to facilitate ECOG strip merging.
31 Jul 2013, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 4 (BUG_FIX)
fixed failure to apply a negative dilation in non-convert case
Thanks to W Gaggl for noting the problematic scenario.
26 Jul 2013, RW Cox, 3dNwarpFuncs, level 2 (MINOR), type 1 (NEW_PROG)
Calculate various functions of a warp (e.g., Jacobian)
19 Jul 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
-resample and -allinfast options
For resampling (without registering) and fast affine registering -- both
done via 3dAllineate.
19 Jul 2013, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
applied ITK compatibility updates from 11/2010 by H Johnson
18 Jul 2013, RC Reynolds, @move.to.series.dirs, level 2 (MINOR), type 6 (ENHANCE)
added -dprefix option, for output directory prefix
16 Jul 2013, RW Cox, 3dQwarp, level 3 (MAJOR), type 2 (NEW_OPT)
-allineate = run 3dAllineate first
With this option, 3dQwarp can align datasets that are not so close, and
are not on the same 3D grid (since the substitute source dataset output
by 3dAllineate will be on the base grid).
16 Jul 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
added checks for early python versions; added a little help
11 Jul 2013, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 1 (NEW_PROG)
perform many checks to validate a system for AFNI use
09 Jul 2013, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -ushort2float, for converting unsigned shorts to floats
Requested by D Handwerker.
09 Jul 2013, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
added more info for locating bad chars with -test
09 Jul 2013, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
if unsigned shorts are detected, add -ushort2float to to3d command
07 Jul 2013, RC Reynolds, @Install_FATCAT_DEMO, level 2 (MINOR), type 1 (NEW_PROG)
replaces @Install_PTaylor_TractDemo
28 Jun 2013, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added get/show_process_stack(), get/show_login_shell()
Can use these from command line, e.g. :
afni_util.py -eval 'show_login_shell()'
afni_util.py -eval 'show_login_shell(verb=1)'
afni_util.py -eval 'show_process_stack()'
27 Jun 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_mot_as_ort
Applies motion regressors via -ortvec, a potential future change.
26 Jun 2013, RW Cox, various files, level 2 (MINOR), type 0 (GENERAL)
Allow individual sub-bricks over 2 GB in size
By changing the brick_bytes[] array to int64_t from int, and then
modifying all places that use it.
25 Jun 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_motsim and -volreg_opts_ms
10 Jun 2013, RC Reynolds, @simulate_motion, level 2 (MINOR), type 6 (ENHANCE)
added warp_methods, etc.
10 Jun 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
added -select_groups, -show_cormat, -volreg2allineate
04 Jun 2013, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
Added nearest neighbor search option
There is no need to search along a certain direction when
mapping between two spheres of identical radius and size.
31 May 2013, RC Reynolds, @simulate_motion, level 3 (MAJOR), type 1 (NEW_PROG)
program to create time series simulated by motion parameters
14 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 2 (NEW_OPT)
New -plusminus option
'Meet-in-the-middle' matching: base(x-dis(x)) = source(x+dis(x)).
For application to unwarping blip-up and blip-down EPI datasets.
Also, fix bug when -no?dis options are used -- when the code for
parameter sub-vector mapping was moved around, the 'free' call to get
rid of any old mapping wasn't moved with it -- bad Bob, bad bad bad.
14 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -show_argmin/max
14 May 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Renamed motion files for -save_vr without -epi2anat
13 May 2013, RC Reynolds, @RenamePanga, level 2 (MINOR), type 4 (BUG_FIX)
added -column to count commands writing listfile
There is a 4096 byte limit in addto_args(), which could be made dynamic.
10 May 2013, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
named glob functions as afni_*; R was using sys funcs, rather than local
09 May 2013, ZS Saad, R_io, level 2 (MINOR), type 4 (BUG_FIX)
Temporary fix of segfault happening in R from R_io.so
Source of problem is a call to COMPRESS_setup_programs()
Not sure why the following crash was happening:
*** caught segfault ***
address 0x3800000100, cause 'memory not mapped'
However a temporary env. SKIP_COMPRESS_SETUP will get around it.
09 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -write_3dD_script and -write_3dD_prefix
08 May 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -rank, -rank_style, -reverse_rank
07 May 2013, DR Glen, 3dAnatNudge, level 2 (MINOR), type 5 (MODIFY)
always produce output with -prefix even if no shift
06 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added -regress_anaticor example; opt implies -mask_segment_anat/_erode
06 May 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
added option -slice_timing
03 May 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -regress_anaticor and -mask_segment_erode
Use the -regress_anaticor option to regress the WMeLocal time series.
This is the ANATICOR method of HJ Jo.
01 May 2013, RW Cox, 3dQwarp, level 2 (MINOR), type 5 (MODIFY)
Minor updates
Make -emask work with -duplo.
Add SAMPLE USAGE section to help to show how to combine 3dAllineate with
3dQwarp, and/or align_epi_anat.py also.
Add -base and -source options, to make program look more like 3dAllineate.
26 Apr 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_trs_censored/_uncensored (mostly for X-matrix datasets)
24 Apr 2013, RC Reynolds, @move.to.series.dirs, level 2 (MINOR), type 1 (NEW_PROG)
partition a list of DICOM files by series number
Done for I Shapira.
24 Apr 2013, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 4 (BUG_FIX)
did not set 'ver' before goto START
Thanks to I Schwabacher for noting the problem and fix.
24 Apr 2013, RC Reynolds, 3dinfo, level 2 (MINOR), type 4 (BUG_FIX)
allow -space for nifti; actually exit if -view and result exists
Thanks to I Schwabacher for noting the problem and fix.
23 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added eroded ROIs for -regress_ROI: WMe, GMe, CSFe
22 Apr 2013, ZS Saad, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Added -out1D option to output correlations in text format.
22 Apr 2013, RW Cox, 3dNwarpAdjust, level 2 (MINOR), type 1 (NEW_PROG)
For template-building via @toMNI_Qwarp
Computes the mean warp, and adjusts the individual warps to get rid of
this mean warp (under the presumption that it is some kind of bias).
22 Apr 2013, RC Reynolds, auto_warp.py, level 2 (MINOR), type 0 (GENERAL)
modified afni_base.afni_name.new() with 2 cases of parse_pref=1
This is currently the only application of that parameter.
19 Apr 2013, DR Glen, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
lpi xyz output option
17 Apr 2013, RC Reynolds, 3dAFNItoNIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed old use of use of strcat() after strdup()
Thanks to B Benson and J Stoddard for noting the problem.
17 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_vr result causes crash
16 Apr 2013, RC Reynolds, 3dmaxima, level 2 (MINOR), type 4 (BUG_FIX)
modernize dataset coordinate reporting, using proper signs
Thanks to G Pagnoni for reporting the issue.
16 Apr 2013, RC Reynolds, 3dmaskave, level 2 (MINOR), type 2 (NEW_OPT)
added -sumsq (sum squares) and -enorm (Euclidean norm) options
12 Apr 2013, RW Cox, 3dLocalHistog, level 2 (MINOR), type 1 (NEW_PROG)
Collecting counts of labels in nbhd of each voxel
For building atlases that allow for uncertainty in position
09 Apr 2013, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added options for providing orts for each input time series
See options -*_orts in the help output.
09 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed computed fitts for REML case (was from 3dDeconvolve)
Thanks to G Pagnoni for noting the problem.
05 Apr 2013, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
added Help web link to class handouts
05 Apr 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
revert -save_orig_skullstrip to -save_skullstrip
This should have no effect on results, except for rename of anat_strip
to anat_ns. It also gets around a temporary name change from AEA.py.
04 Apr 2013, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -Apair option
For testing differences in correlations in 1 group from 2 different
seeds -- the regular seed minus the 'Apair' seed. Also changes to AFNI
to set the Apair seed, etc.
01 Apr 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
motion file renamed
Some output files like the motion files were accidentally renamed.
29 Mar 2013, DR Glen, general compression, level 2 (MINOR), type 3 (NEW_ENV)
pigz for faster gzip-like compression
pigz is a gzip utility that makes use of multiple CPU's.
It produces and uses .gz files. To use, set AFNI_COMPRESSOR to PIGZ.
27 Mar 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_group_labels, -label_prefix_keep/_drop
Option -label_prefix_drop can be used to remove bandpass regs for 3dRSFC.
27 Mar 2013, DR Glen, 3dBrickStat, level 2 (MINOR), type 2 (NEW_OPT)
absolute value of voxels for statistics
26 Mar 2013, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added option -inflate for automatic creation of semi-inflated surfaces
See @SUMA_Make_Spec_FS -help for details
26 Mar 2013, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add option -cmeth (MEAN or MEDIAN) for Steve Gotts
25 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Merged handling of CoordBias with Prying, all in VisX
Lots of annoying little details there. See functions like:
SUMA_*CoordBias*, SUMA_ApplyVisXform(), and SUMA_Apply_VisX_Chain()
25 Mar 2013, P Taylor, 3dReHo, level 2 (MINOR), type 2 (NEW_OPT)
More voxelwise neighborhood shapes available.
Voxelwise neighborhoods can be any sphere/radius size, and even
ellipsoidal. Some memory stuff should be better as well.
22 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added stippling for line segments DOs, see SUMA's ctrl+h for details.
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Texture demos in DriveSuma were failing.
Problem was a combination of coordinate clipping when frame coords
were at 0 or 1. That is now fixed. Also, demo.*do files needed changing
to move texture on surface into mobile.niml.do
Depth test is no longer disabled with textures.
20 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Text was not appearing at times. Bug was in SUMA_SO_NIDO_Node_Texture()
19 Mar 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Prying was off for new GIFTI standard-mesh surfaces.
Bug was caused by a failure to identify LR sides of GIFTI
surfaces. SUMA was not preserving the side of a GIFTI surface
at write time in SUMA_GIFTI_Write(). Code was also modified
to guess the side of pre-existing GIFTI surfaces.
Prying was also off when a transform was found in the header
of the surface volume because dimensions were not being recomputed
after applying the VolPar transform. That is now fixed.
19 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
alignment AddEdge error
Error in resampling step of AddEdge procedure causes crash.
Problem requires both -giant_move (or -prep_off or -resample off) and
-AddEdge.
14 Mar 2013, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
NearestNodeCoords was added to -output_params
14 Mar 2013, P Taylor, 3dNetCorr, level 4 (SUPER), type 1 (NEW_PROG)
New function: calculate correlat/Z of ROIs in a network.
This program works on several networks as separate subbricks simultan-
eously.
14 Mar 2013, P Taylor, rsfc, level 2 (MINOR), type 5 (MODIFY)
New functions; streamline some other functions.
For addition of 3dNetCorr, mainly.
14 Mar 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 5 (MODIFY)
List ROI labels near start of *.grid; use floor to get NmNsThr
This allows for more similarity with 3dNetCorr, and might be useful
as well if the labeling of ROIs in a network is not just 1,..,max.
The flooring vs ceiling is so that people don't have to use 0.00099
as a relative fraction of MC iterations to get the number they want.
14 Mar 2013, P Taylor, 3dDWUncert, level 2 (MINOR), type 4 (BUG_FIX)
Silly bug in e_{13}^* estimation.
Mean and std of uncertainty of e1 toward e3 was buggy.
12 Mar 2013, RW Cox, 3dNwarpApply, level 2 (MINOR), type 2 (NEW_OPT)
Various fixes
-ainterp = lets you interpolate data differently from warp
-affter = lets you use a different affine warp for each sub-brick
-nwarp = allow catenation and inversion directly on the command line
These last 2 options make the program 3dNwarpCat pleonastically
redundant.
12 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
Handling input and output directories
Output now goes to current directory (./) unless otherwise specified
with -output_dir. Thanks a lot, Rick.
11 Mar 2013, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
Handling input and output directories
Output follows input directories unless specified with -output_dir
Previously, all input files had to exist in current directory.
Changes allow for output to follow anat or epi dataset directories
or specified output directory. Also minor change to call tcsh without
sourcing startup .cshrc
11 Mar 2013, DR Glen, @Atlasize center of mass, level 2 (MINOR), type 2 (NEW_OPT)
Add -centers for center of mass locations in atlas regions
-centers option added to @Atlasize and @MakeLabelTable
This location is simple center of mass for now and may be
outside region for non-blobbish regions
08 Mar 2013, RC Reynolds, 3dTcat, level 2 (MINOR), type 2 (NEW_OPT)
added -TR and -tpattern options
07 Mar 2013, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
handle -prefix and -overwrite for -show_bad_backslash
The combination can be used to 'fix' bad files.
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Prying hemispheres apart to see medial or lateral sides simultaneously
This is controlled via the ctrl+Button 1-Motion. See SUMA's ctrl+h output
for details. The prying behaviour is different for spheres and flat maps
Just try it and see. ctrl+double click to get back to initial view.
See also env: SUMA_LHunify
22 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Automatically adjust position of LR surfaces so that they don't overlap
This is only done for anatomically incorrect surfaces, the others should
not overlap of course. This allows for simultaneous viewing of inflated
surfaces and flattened ones side by side.
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Option -anatomical labels all -i_* -t_* surfs anatomically correct
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Option -onestate put all -i_* surfs on command line in the same state
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed FOV problems for auto setting and fixing zoom level across states
22 Feb 2013, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LHunify to automatically merge LR hemispheres in all views
This is done by discarding the _lh _rh to state names that are
created by @SUMA_Make_Spec_FS
22 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Instead of just individual ROI masks, can get map of Ntracks/voxel.
This allows a posteriori thresholding/comparisons/analysis.
20 Feb 2013, RW Cox, 3dUnifize, level 2 (MINOR), type 1 (NEW_PROG)
Quick and dirty approximate spatial uniformization of T1 anats
Mostly for use with 3dQwarp
19 Feb 2013, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Histogram plugins can now do cumulative distributions
set AFNI_HISTOG_CUMULATIVE to YES
15 Feb 2013, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Added -FNameNoAfniExt to -out option
15 Feb 2013, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Allowed script to work with NIFTI input for both -surf_anat and -exp_anat
14 Feb 2013, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Added stippling-based transparency to surface viewing.
Fancier blending-based transparency will have to wait.
14 Feb 2013, ZS Saad, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 2 (NEW_OPT)
Option -nocor to improve data import from FreeSurfer
Option avoid COR images, produces NIFTI and GIFTI output that
aligns with the initial volume passed to FreeSurfer. This required
considerable changes to the script and will not be the default for
a while longer.
14 Feb 2013, ZS Saad, apsearch, level 2 (MINOR), type 5 (MODIFY)
Improved parsing for options to avoid getting options from sample commands
Previously, if you used an example in the help that called
a different program and you used options on clean lines as part of that
example command, those options would get attributed to the program
whose help you're reading. Pfew. Not anymore.
14 Feb 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -TransMode to control surface transparency.
13 Feb 2013, RC Reynolds, unix_tutorial, level 3 (MAJOR), type 1 (NEW_PROG)
added tutorial to CVS tree, with processed files under AFNI_data6
07 Feb 2013, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
Added Greg Baxter's (UCSD) change for b-matrix input
06 Feb 2013, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merged Paul Taylor's recent code changes
Also created afni_history_ptaylor.c
see afni_history -author ptaylor for details on the changes
06 Feb 2013, ZS Saad, MakeColorMap, level 2 (MINOR), type 2 (NEW_OPT)
-suma_cmap, -usercolutfile, and -sdset* options for SUMA colormaps
The new options allow users to create SUMA's colormaps with labels
and turn datasets into labeled datasets with the user's colormap
06 Feb 2013, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-labelize for assigning a SUMA colormap to an integral valued dset
06 Feb 2013, P Taylor, 3dProbTrackID, level 2 (MINOR), type 2 (NEW_OPT)
Add ability to output each WM-region mask as an individual ROI.
This should make it simpler to use an ROI as a mask than
with the 2^(ROI number) labelling system within subbrick outputs.
30 Jan 2013, RC Reynolds, python-general, level 2 (MINOR), type 6 (ENHANCE)
added less biased correlations and various gcor utility functions
24 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
be able to process a run of AFNI volumes (-file_type AFNI)
added for Der-Yow Chen and Cecil Yen
22 Jan 2013, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Added -bash option for bash filename completion, & -recreate_all_afni_help
Thanks be to Isaac Schwabacher.
22 Jan 2013, ZS Saad, HalloSuma, level 2 (MINOR), type 1 (NEW_PROG)
A sample light-weight program to illustrate 2-way communication with AFNI
The program can be compiled in C or C++ along with the NIML library
without having to link to AFNI/SUMA libraries.
Documentation is the code.
22 Jan 2013, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -echo_nel(*) option to show NIML communication elements
22 Jan 2013, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Added -hand for handeness of orientation
22 Jan 2013, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -file_type, in prep for reading AFNI/NIfTI images
18 Jan 2013, RC Reynolds, @compute_gcor, level 2 (MINOR), type 1 (NEW_PROG)
compute GCOR = global correlation of a dataset
16 Jan 2013, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -dc_params
To go with new scripts AFNI_data6/realtime.demos/demo.2.fback.*.
16 Jan 2013, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -show_gcor (and _all and _doc)
compute GCOR (average correlation) on 1D files
11 Jan 2013, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
Added -flip_orient option to change orientation of triangles.
09 Jan 2013, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -regress_compute_gcor
If errts and EPI mask exist, GCOR is computed by default.
07 Jan 2013, ZS Saad, 3dinfill, level 2 (MINOR), type 2 (NEW_OPT)
Added -radial_* options to test SUMA_Volume_RadFill() function.
07 Jan 2013, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added option -l2norm, to compute L2 norm
04 Jan 2013, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would make 3drefit exit if dataset contains a warpdrive attribute
02 Jan 2013, RW Cox, afni Clusterize, level 2 (MINOR), type 5 (MODIFY)
Allow use of Spearman rather than Pearson for scatterplot correlation
Set via environment variable AFNI_CLUSTER_SPEARMAN, or by popup menu
attached to top of clusterize report form. This is for PK.
21 Dec 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 4 (BUG_FIX)
change check for recur download by looking for known string in script
Thanks to S Lowell for reporting the error.
20 Dec 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 4 (BUG_FIX)
remove -volreg_tlrc_warp in case of no tlrc block
Thanks to P Taylor for reporting the error.
19 Dec 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL)
Update from Rayus for handling .nii files.
18 Dec 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
have THD_subbrick_minmax fall back to THD_slow_minmax_dset if no STAT
This is a fix for 3dSkullStrip on NIfTI dsets.
Thanks to kelvin for reporting the error.
05 Dec 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
add Detrend button to Opt menu
Detrends each time series before plotting. For Javier.
29 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
add -f to 'tcsh -c' for getting output from commands
Thanks to P Molfese for the suggestion to avoid .cshrc text output.
28 Nov 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
-dospcov
Compute Spearman correlation of subject results with covariate. Output
sub-bricks are labeled with '_SP' at the end, as in 'LLL_cov_SP' to
indicate the group with label 'LLL' correlated with the covariate with
label 'cov'. This is for the IMom (PK).
26 Nov 2012, RC Reynolds, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
added -save_script option
added script history in afni_com class
23 Nov 2012, RW Cox, afni instacorr, level 2 (MINOR), type 5 (MODIFY)
Allow Start and End indexes, rather than Ignore (=Start)
To allow Instacorr-ing a subset of a time series. Per the request of
the Exceptional Javier Gonzalez-Castillo
15 Nov 2012, ZS Saad, AFNIio.R, level 2 (MINOR), type 5 (MODIFY)
Made read.AFNI and write.AFNI more clever
Changes included: AUTO method selection, dset.attr() improvements
to handle dset structures or their headers from either clib or Rlib
functions. Micro change to THD_dblkatr_from_niml which crashed for
null strings.
15 Nov 2012, RC Reynolds, 3dTqual, level 2 (MINOR), type 2 (NEW_OPT)
added -mask option
Requested by evangelou.
14 Nov 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed check for random space in -max_consec case
Thanks to Kristina for reporting the error.
13 Nov 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fixed fopen_maybe to check for .1D suffix on file streams
Suffix might get added by EDIT_dset_items.
Thanks to I Schwabacher for reporting the error.
12 Nov 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT)
Straight and weighted divisions of T1 by PD, and initial alignment
The weighted volume allows one to keep the high-res. aspect of
PD division, while considerably reducing the extreme enhancement.
12 Nov 2012, ZS Saad, 3dHist, level 2 (MINOR), type 2 (NEW_OPT)
Added -cmask and -quiet to 3dHist
09 Nov 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash on OSX 10.7_64 apparently caused by gcc's optimization
The fix entailed adding -O1 to target SUMA_xColBar.o in SUMA's
SUMA_Makefile_NoDev. I also changed the way SurfaceControllers
are put away. They are now minimized thus keeping the widgets
realized.
06 Nov 2012, ZS Saad, 3dkmeans, level 2 (MINOR), type 2 (NEW_OPT)
Added -write_dists to only output ascii files when users want them
The changes were made to also cleanup the output of 3dSeg.
06 Nov 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 2 (NEW_OPT)
Added -head*, and -cut_below options to generate whole head masks
This was needed because 3dAutomask or 3dSkullStrip would fail atcreating w
hole head masks for cases with coil-array shading problems
and/or lots of noise.
23 Oct 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
forgot to leave show_size_n_offset set
Thanks to J Jarcho for reporting the to3d failure.
19 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
added test for BOM bytes (byte order mark)
19 Oct 2012, G Chen, 3dMVM, level 3 (MAJOR), type 1 (NEW_PROG)
Multivariate modeling approach to group analysis
This is an R program that performs conventional ANOVA or
ANCOVA-type analysis with no limit on the number of variables.
See more details at https://afni.nimh.nih.gov/sscc/gangc/MVM.html
18 Oct 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 4 (BUG_FIX)
small updates to correspond with library changes
18 Oct 2012, RC Reynolds, file_tool, level 2 (MINOR), type 6 (ENHANCE)
added convenience option -test
17 Oct 2012, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT)
added -no_length option, which helps when running diffs on output
16 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed functions that generate volume masks from surfaces
There was a bug in SUMA_FindVoxelsInSurface() and SUMA_SurfGridIntersect()
which made for ugly masks in the fast mode. This is no longer the case,
SUMA_FindVoxelsInSurface() is about as good as its sister function
SUMA_FindVoxelsInSurface_SLOW(), but considerably faster.
This bug fix might affect some 3dSkullStrip and 3dSurfMask results. The
more voxel sizes differ from 1x1x1, the more noticeable the difference
might be.
16 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added analysis type and processing block list
16 Oct 2012, DR Glen, afni show atlas colors, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug that would crash afni if paned color and show atlas colors
15 Oct 2012, ZS Saad, @T1scale, level 2 (MINOR), type 2 (NEW_OPT)
A better masking option using -brainhull
The option seems pretty good at creating brain mask from pretty
lousy data.
13 Oct 2012, ZS Saad, 3dHist, level 2 (MINOR), type 1 (NEW_PROG)
Computes histograms using functions from the segmentation routines
The program uses heuristics to automatically select histogram
parameters, and it allows histogram queries.
It had to be separate from 3dhistog because it uses libSUMA.a and because
the latter's interface was getting too complicated.
12 Oct 2012, ZS Saad, 3dedge3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed scaling problem for short/byte data.
12 Oct 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added byte-swapping for complex numbers in thd_niml.c
09 Oct 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allow input of surface-based complex time series.
SUMA will report and graph the magnitude of complex data
Other transformations can be added when needed.
Surface data I/O were modified to allow handling
of complex-typed data including functions in thd_niml.c, and thd_gifti.c
Programs like 3dDFT and 3dcalc can read/write complex surface-
based datasets.
09 Oct 2012, ZS Saad, 3dDFT, level 2 (MINOR), type 2 (NEW_OPT)
Allow handling of complex surface-based data
Earlier versions could not output complex data for surface-based datasets.
Minor changes to the help output to fix order of -cx2r option and
allow option suggesting.
05 Oct 2012, RC Reynolds, dicom_hinfo, level 2 (MINOR), type 2 (NEW_OPT)
added option -no_name
05 Oct 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -quick_censor_count
04 Oct 2012, ZS Saad, afni-matlab, level 2 (MINOR), type 2 (NEW_OPT)
Minor tweaks to WriteBrik and BrikInfo
WriteBrik can automatically set some header fields (AdjustHeader option)
BrikInfo now loads IJK_TO_DICOM_REAL
03 Oct 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
dashed parameters are now illegal for many options in many python programs
Affects programs:
1d_tool.py, afni_proc.py, gen_group_command.py, make_random_timing.py,
make_stim_times.py, option_list.py, timing_tool.py
02 Oct 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
added stim_type column to stim table
This corresponds to the afni_proc.py option -regress_stim_types.
01 Oct 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added 'file' to list of -stim_types parameters
The 'file' type would imply -stim_file in 3dDeconvolve, not timing.
28 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's map_TrackID to warp tracks by an affine transform
28 Sep 2012, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT)
Enabled automatic centering via -init_xform
You can use -init_xform AUTO_CENTER or -init_xform CENTER
to perform center alignment during registration.
28 Sep 2012, ZS Saad, @T1scale, level 2 (MINOR), type 1 (NEW_PROG)
A mini script to scale T1s by PD volumes
Script uses method borrowed from @CalculateSignatures
to reduce bias field in T1 using a PD volume. Script also
works well without PD.
26 Sep 2012, RC Reynolds, nifti_tool, level 2 (MINOR), type 4 (BUG_FIX)
changed ana originator field from char to short
26 Sep 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 2 (NEW_OPT)
added -apsearch; verify download for recursive step
25 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use errts_REML to compute blur if 3dD_stop; apply compute_fitts if no reml
Thanks to P Molfese for reporting the problem.
20 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added some projection function to python libraries
19 Sep 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -scale option for the Person from Kolkata
18 Sep 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Checked in Prantik Kundu's MEICA tools.
Try meica.py -help, also try @Install_MEICA_Demo
13 Sep 2012, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT)
Added -pdf to 3dhistog to make area = 1
13 Sep 2012, RC Reynolds, afni_util, level 2 (MINOR), type 6 (ENHANCE)
can call list functions via -listfunc (to avoid input formatting)
Also, use -join after the LISTFUNC to remove list format on output, e.g.
cd AFNI_data6
afni_util.py -listfunc list_minus_glob_form -join group_results/OLSQ*.HEAD
13 Sep 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
download and run the current version on the web site
Good idea, Bob.
11 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Began merger of surface controllers
The idea is to have all surface controllers in one window
in order to save on screen space. Looks promising but must be
rolled out carefully because surface controllers permeate everything.Use e
nvironment variable SUMA_SameSurfCont to turn feature on.
Make sure it is debugged with valgrind too.
11 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed 'potential' crash in SUMA_SetScaleThr_one()
10 Sep 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Typing in sub-brick arrow fields was ignored on linux
Problem due to incorrect error checking from strtod()
06 Sep 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added -no_volreg for time series already registered
06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
if varying facs/types on NIfTI write, write floats instead of failing
06 Sep 2012, RC Reynolds, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
apply global opt -pad_to_node when going through AFNI format in thd_niml.c
05 Sep 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT)
Added possibility to scale by top percentiles with -FATscl
This would produce .sc9 outputs. It looks like the scaling is
more promising than by MEDIAN(20) or MAD(20).
05 Sep 2012, ZS Saad, 1dRplot, level 2 (MINOR), type 2 (NEW_OPT)
Made program take in histograms produced by 3dGenFeatureDist
This required changes to AFNIio.R so that NIML groups are not
automatically sent to the distbin. Instead, the first element
in the ni_group is returned.
04 Sep 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
Made program output niml 1D format, makes it easy to plot with 1dRplot
04 Sep 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -regress_ROI
This allows for tissue-based regression, with ROI averages from any of:
brain (from full_mask), GM, WM and CSF (from Classes_resam)
The 'mask' block is required for all ROIs, and option -mask_segment_anat
is required for the latter 3.
31 Aug 2012, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added option -signed_absmax
Requested by P Hamilton.
30 Aug 2012, ZS Saad, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
Made program create corr. matrix as opposed to just one pair of sub-bricks
Output is also beautified with option -show_labels
29 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Allowing yoking of intensity to node selection.
Ctrl+Button-3 would select a node and switch intensity sub-brick
to that node's index * K. This is only done if the dataset currently
viewed has as K times as many sub-bricks as the surface has nodes.
K being an integer, naturally.
Nick Oosterhoff instigated this business
29 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI build was failing on machines where DONT_USE_MCW_MALLOC was defined
The cause of failure was a missing #define NI_calloc() when
DONT_USE_MCW_MALLOC is defined. The one line needed is now in niml.h.
Builds likely affected are solaris and macosx_10.7_Intel_64
Affected build dates from about Aug. 24th to Aug. 29th.
24 Aug 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Added interactive clustering to surface controller
The state of affairs:
-Clustering tables are only output to the terminal
and the log window.
-Clustering is yoked between hemispheres
-Can control connectivity radius and min area or min nodes
-When you click on a node inside a cluster, the node in that
cluster with the highest value is highlighted with a black
sphere.
24 Aug 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's 3dRSFC to the distribution
24 Aug 2012, ZS Saad, @CalculateSignatures, level 2 (MINOR), type 2 (NEW_OPT)
Added coordinate feature generation, if TLRC xform is provided
Note that the TLRC xform need not be too precise. The coordinate
features are not intended to make sure of segmentation templates.
24 Aug 2012, RC Reynolds, column_cat, level 3 (MAJOR), type 1 (NEW_PROG)
like 'cat', except horizontally (see recent Unix command, 'paste')
23 Aug 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 2 (NEW_OPT)
can pass -censor_dset
15 Aug 2012, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT)
Added -sublabel_prefix and -sublabel_suffix
14 Aug 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
match default class order for 3dSeg; copy labeltable into resampled dset
14 Aug 2012, DR Glen, whereami minimum probability, level 2 (MINOR), type 2 (NEW_OPT)
Minimum probability option to consider for probabilistic atlases
Can set option, -min_prob, or environment variable,
AFNI_WHEREAMI_PROB_MIN, to control output of whereami reports or
masks from probabilistic atlases
14 Aug 2012, DR Glen, 3drefit -epan error, level 2 (MINOR), type 4 (BUG_FIX)
Removed error for refitting data type
3drefit would exit with error for -epan and multi-subbrick data
Removed incorrect checks against archaic timepoints per TR nvals
10 Aug 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 0 (GENERAL)
Updates from Rayus.
Fixed bugs with -outcensor and -snr.
Added -bpassregs and -keepuncensored.
Use variable detrending for -tsnr.
08 Aug 2012, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Improved handling of coords in 'cm' units and better axis text layout
Surfaces with coords in cm were poorly displayed and without warning.
Now you are urged to make use of the SUMA_NodeCoordsUnits env .
Axis text labels were also improved to reduce clobbering.
08 Aug 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_slice_loc; fixed app of use_last_elem in mri_read_dicom
g_info.use_last_elem has usurped the lone global
06 Aug 2012, DR Glen, NIFTI reading, level 2 (MINOR), type 3 (NEW_ENV)
Handling view equivalents for NIFTI
AFNI_NIFTI_VIEW sets default view for AFNI datasets marked as
'aligned' (sform_code or qform_code = 2). This variable should
be set to 'TLRC', 'ORIG' or 'ACPC'.
31 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
have -mask_segment_anat default to no (libgsl is not quite so common)
31 Jul 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
speed up reading NIfTI files with long histories (THD_dblkatr_from_niml)
Thanks to J Gonzalez for reporting the problem.
31 Jul 2012, RC Reynolds, 3dresample, level 2 (MINOR), type 4 (BUG_FIX)
update IJK_TO_DICOM and _REAL at end of resample library function
Thanks to I Schwabacher for reporting the IJK_TO_DICOM discrepancy.
30 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if surface analysis, create run_suma script
30 Jul 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_mmms
Display min, mean, max, stdev of each column.
26 Jul 2012, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_comm_times option to show communication times
Added for J Evans (and to get it off an ancient todo list).
26 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -mask_segment_anat and -mask_rm_segsy
If anat is stripped, create segmented anat unless user says not to.
26 Jul 2012, RC Reynolds, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
K text columns (after label) would result in K lost float columns
Thanks to Phoebe of Harvard for reporting the problem.
19 Jul 2012, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
Allow for L/R hemi yoking for many operations
These include:Threshold setting. I,T,B sub-brick selection. Range
setting. Dset loading. Cmap changing. Dset switching.
Order changing.
18 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 1 (NEW_PROG)
Added Paul Taylor's 3dReHo to the distribution
17 Jul 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
added checks for volreg and uncensored X-mat; get view from volreg
11 Jul 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
fill gaps and holes in anatomical masks
(now requires AFNI from 7 May, 2012)
10 Jul 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made default prefix path be ./ instead of path of input
The change was done to function EDIT_empty_copy() which assigned
to a pathless prefix the path of the input dataset if the latter
was specified. The problem was that something like:
3dMean -prefix mmm P1/joe+orig P2/jane+orig
would have written mmm+orig under P1/
To make matters less palatable other programs like 3dcalc behaved
differently: 3dcalc -prefix ccc -a P1/joe+orig -expr 'a'
would produce ./ccc+orig
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Use ArrowFields when datasets have large numbers of sub-bricks
The switch is done automatically and is controlled with env:
SUMA_ArrowFieldSelectorTrigger
06 Jul 2012, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ArrowFieldSelectorTrigger set threshold for using ArrowFields
For datasets with sub-bricks >= SUMA_ArrowFieldSelectorTrigger
and arrow field is used to switch between sub-bricks
29 Jun 2012, RC Reynolds, @Install_RSFMRI_Motion_Group_Demo, level 2 (MINOR), type 1 (NEW_PROG)
program is for installing demo of RSFMR on big and small motion groups
28 Jun 2012, ZS Saad, ROIgrow, level 2 (MINOR), type 2 (NEW_OPT)
Added -insphere and -inbox options
These options grow ROIs by finding nodes that fall inside a box or sphere
of preset size around nodes in the original ROIs.
28 Jun 2012, DR Glen, Draw Dataset plugin, level 2 (MINOR), type 4 (BUG_FIX)
Resampling of atlas regions to lower resolution undercounted
Draw Dataset plugin atlas resampling to a lower resolution dataset
undercounts number of voxels. Incorrect usage of temporary volume
in byte storage was fixed with float volume. Additionally, new
environment variable, AFNI_DRAW_THRESH, allows for variable
threshold level (done with RCR)
22 Jun 2012, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
added commands 3dANOVA2 and 3dANOVA3; added option -factors
Need to add help for -factors (i.e. for 3dANOVA3 -type 4).
19 Jun 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Ctrl+W was not saving datasets when filenames contained a path
Problem had to do with clumsy prefix forming.
19 Jun 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -switch_cmode to allow switching how values map to colors
This controls the 'Col' menu in SUMA's surface controller.
19 Jun 2012, RW Cox, 3dttest++, level 2 (MINOR), type 0 (GENERAL)
Internal wildcard expansion with SHORT FORM '-set' options.
15 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_extern
15 Jun 2012, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
make num_dim violation a warning, because of mris_convert
05 Jun 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
warn users if married types and files do not seem to match
31 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merged ptaylor's code changes into the distribution
30 May 2012, DR Glen, 3dinfo, 3drefit, level 2 (MINOR), type 5 (MODIFY)
av_space option handling and orig/other space refitting
3dinfo reports view extension for -av_space instead of generic
space view extension. 3drefit will warn if setting non-orig
space on orig view data or orig space on tlrc view data.
25 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
display modified options and subject defaults
24 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Merger of changes in P. Taylor's code
24 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
csf_val and csf_fa options apply to linear solutions too
23 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -clust option, to allow 3dClustSim stuff to be used
23 May 2012, DR Glen, 3dinfo, @auto_tlrc, level 3 (MAJOR), type 4 (BUG_FIX)
Generic space handling corrected for TT_N27 and other spaces
@auto_tlrc would crash with improper generic spaces
Generic space restricted to AFNI view names (orig, acpc, tlrc)
22 May 2012, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added regress_bandpass and regress_mot_deriv (probably for resting state)
22 May 2012, DR Glen, 3dDWItoDT, level 2 (MINOR), type 2 (NEW_OPT)
csf_val and csf_fa options for default values if B=0 less than gradient values
21 May 2012, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Made program output mapping info file for use with SurfToSurf
Also made microscopic improvement to automatic dset name generation for -d
set_map
21 May 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Made the script also port thickness data and take them to std. space
21 May 2012, ZS Saad, 3dTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Added -covariance option, turned off DOF setting for anything but pearson.
See function THD_covariance()
21 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added the long-desired-but-not-so-needed -regress_stim_types option
This allows users to specify -stim_times/_AM1/_AM2/_IM.
17 May 2012, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -donocov option
When -covariates is used, -donocov says to also do the NO covariates
analyses and tack them onto the end of the results -- for comparison fun
15 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
Added '[1dcat FF.1D]' syntax for sub-brick selections in 1D file
This was added for the same reason '[count ...]' was added, and
that is to allow for lengthy selection values. Dealing with selections
of 100+ sub-bricks virtually guarantees some string limit is reached,
somewhere. See 3dTcat -help for details
11 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
also output average censored per-TR motion
10 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
allow for a wider range of file names
- handle case of more than 99 runs
- look for files of the form *_rall.1D, as well as *.rall.1D
10 May 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow processing of more than 99 runs
08 May 2012, ZS Saad, count, level 2 (MINOR), type 2 (NEW_OPT)
Added -form to count: count -form %c 49 130
08 May 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Code updates for P. Taylor's tractography
08 May 2012, ZS Saad, 3dSeg, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory leak problem
07 May 2012, RC Reynolds, 3dmask_tool, level 2 (MINOR), type 6 (ENHANCE)
replaced THD_mask_erode with new THD_mask_erode_sym
This change should make dilate and erosion operations symmetric.
07 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added weighted_enorm method for -collapse_cols; added -weight_vec
07 May 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Coordinate transformations in atlas access
Coordinates were not transformed properly if an inverse affine
transformation was required for the case of atlases in another
space than the dataset.
07 May 2012, DR Glen, NIFTI input/output, level 2 (MINOR), type 5 (MODIFY)
NIFTI qform/sform codes from generic space of template space
qform and sform codes are set by string in generic space, not template
space, of input dataset. For example, TT_N27 spaces will be marked for
NIFTI output as TLRC. NIFTI data with any non-ORIG or ACPC space will
be marked as an 'aligned' space in NIFTI with the sform and qform codes.
Currently only TLRC/MNI/Aligned are supported spaces in NIFTI standard.
'aligned' space datasets will be interpreted as equivalent to TLRC view
datasets. See AFNI_atlas_spaces.niml for space definitions that include
generic space names.
04 May 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added inverse distance measures to InstaCorr
For the moment, those options are only accessible to usernames
rwcox and ziad. Relevant functions are:
THD_vectim_distance(), and THD_distance(). THD_distance() is not
used at the moment, it would be from 3dLocalBistat once I get around
to testing it. For now, its access from 3dLocalBistat is #if-ed out.
04 May 2012, RC Reynolds, afni_restproc.py, level 2 (MINOR), type 4 (BUG_FIX)
submitting updates from Rayus
Updates are in changelog.
03 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -backward_diff and -forward_diff
Note, -backward_diff is the same as -derivative.
01 May 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
allowed -ordered_stimuli and -max_consec, together
Requested by Liat.
01 May 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added -prefix option; added censor coloring to 1dplot commands
01 May 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
added -looks_like_AM
30 Apr 2012, RC Reynolds, afni_restproc.py, level 3 (MAJOR), type 1 (NEW_PROG)
this program is by Rayus Kuplicki, please contact him for information
27 Apr 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added percentile thresholding to AFNI's interface
Relevant functions:
flush_vinfo_sort();
flush_3Dview_sort();
get_3Dview_sort();
AFNI_thresh_from_percentile()
Relevant structure variables:
cont_perc_thr in Three_D_View;
th_sort, N_th_sort, th_sortid in AFNI_view_info;
Feature also accessible from plugout_drive with: SET_FUNC_PERCENTILE +/-
27 Apr 2012, RC Reynolds, 3dmask_tool, level 3 (MAJOR), type 1 (NEW_PROG)
a program to manipulate mask datasets
26 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Made header_name be same as brik_name for NIFTI dsets
Changes were in EDIT_dset_items(), search for April 26
26 Apr 2012, RW Cox, 3dLocalBistat, level 2 (MINOR), type 2 (NEW_OPT)
Allow 1 volume vs. multi-volume; Add slope options
24 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Can read .niml.tract files as DOs. Nothing too fancy yet
Tractography files are loaded and handled like any DO.
See function SUMA_DrawTractDO().
24 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Wrote TrackIO.[ch] to handle tractography data I/O.
All changes are under ptaylor/ . New tract format is in NIML.
See functions in TrackIO.h for details.
24 Apr 2012, ZS Saad, 3dTrackID, level 2 (MINOR), type 5 (MODIFY)
Modified 3dTrackID to make use of new track I/O functions.
24 Apr 2012, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add censor stuff to 1dplot, for Colm
24 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
if surface data with generic prefix, append surf-type suffix
Done to fix ANOVA commands on surface.
Thanks to R Ray for bringing this up.
18 Apr 2012, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Patch BLOCK and dmBLOCK to have their old non-unit-peak behavior
New functions UBLOCK and dmUBLOCK now have the unit-peak behavior.
17 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added atlas/ROI label use with <> range selectors (MCW_get_angle_range)
16 Apr 2012, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
New convenience functions for I/O
SUMA_AddDsetIndexCol(), SUMA_CreateFullDsetPointer, and
macro SUMA_DSET_NAME_CHECK Improved name parsing and format guessing.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
More I/T selector linkage modes.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Show data value at crosshair directly in display
See SUMA_UpdateCrossHairNodeLabelFieldForSO(),
SUMA_FormNodeValFieldStrings(), and SUMA_UpdateNodeValField()
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Better handling on multiline centering for display in viewer window.
16 Apr 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
New option to control which node-based DOs are displayed.
See SUMA's interactive help on 'Ctrl+p' for details.
16 Apr 2012, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Created ptaylor/ under src/ to include Paul Taylor's code contributions
To compile all of Paul's programs: cd src/ptaylor; make all
or from src/ make ptaylor_all
Added macros AFNI_3D_to_1D_index and AFNI_1D_to_3D_index in 3ddata.h
16 Apr 2012, ZS Saad, SurfaceMetrics, level 2 (MINOR), type 5 (MODIFY)
Improved output format and added Displayable Objects to output.
16 Apr 2012, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
Added -closest_possible
For allowing the substitution of the projection result with
the closest node that could be found along any direction.
See changes to SUMA_GetM2M_NN()
16 Apr 2012, ZS Saad, SampBias, level 2 (MINOR), type 5 (MODIFY)
Improved I/O
16 Apr 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -do_draw_mask to restrict where node-based DOs are shown
12 Apr 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
backport to python 2.2
For files that should work on 2.2, avoid sum() and enumerate().
Thanks to L Broster for reporting problems on python 2.2.
08 Apr 2012, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 6 (ENHANCE)
-ordered_stimuli now takes labels
05 Apr 2012, RW Cox, 3dTnorm, level 2 (MINOR), type 1 (NEW_PROG)
Normalize each time series in a dataset
Like 1dnorm for 3D+time datasets
04 Apr 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
if prefix shows STORAGE_UNDEFINED, use BRIK only if not potential surface
22 Mar 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Improve display of node-based DOs. ctrl+p for showing subset of objects.
Node-based DOs overwhelm the display. Ctrl+p allows one to show DOs
only around the selected node, or just at it.
See also DriveSuma's -do_mask_mode option.
22 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Add values at node to the display.
This involved an improvement to the centering of text so that
one can center each line in a paragraph
22 Mar 2012, ZS Saad, @Spharm.examples, level 2 (MINOR), type 5 (MODIFY)
Improvements to the script to make it work with new programe versions.
It will now download its own data for demo purporses.
22 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
apply AFNI_REALTIME_SHOW_TIMES in non-RT feedback case
15 Mar 2012, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added AFNI_REALTIME_Mask_Dset for per-run control over Mask
Also added some missing vars to README.environment.
Done for J Evans.
14 Mar 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_chan and -max_quiet_trs; default sleep = 1.1*TR, max of 2
Added for J Evans and V Roopchansingh.
07 Mar 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
existing package and install dir no longer required for -defaults
06 Mar 2012, RW Cox, 3dNormalityTest, level 2 (MINOR), type 1 (NEW_PROG)
Test voxel values for normality (Gaussianity).
Uses the Anderson-Darling test.
05 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Recorder saving was crashing for very long filenames. Not anymore.
The shell however will not like very long names and will complain.
05 Mar 2012, ZS Saad, afni-general, level 2 (MINOR), type 2 (NEW_OPT)
Added option auto-completion for AFNI's programs for csh users
The implementation of this feature is via apsearch. In particular,
apsearch -update_all_afni_help now creates the necessary commands
for csh's complete program to know about available options.
See apsearch -help for details.
This was done in conjunction with Brian Pittman.
05 Mar 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
EDIT_empty: only propagate writable storage_modes
Added is_writable_storage_mode and DSET_STORAGE_MODE.
Thanks to Eli for reporting the problem.
02 Mar 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
fixed $runs in multi-run ricor
Thanks to I Mukai for reporting the problem.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed suma crash after a plot a certain plot freeze sequence
The sequence was: create plot, freeze it, get another open
then close the frozen one. At this point, suma lost control
of the still unfrozen one, so it is practically frozen.
Pressing Freeze twice on that remaining plot cause suma to crash.
None of that occurs anymore.
01 Mar 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed cutting plane motion while volume rendering under linux
On Macs, the scroll wheel gives out button 6 and 7, on linux
it is Buttons 4 and 5.
01 Mar 2012, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Some cleanups and tweaks of XmHTML library.
Refresh was not working well when scrolling so I ended up adding a mini
refresh routine that seems to do the trick. XmHTMLRefresh(Widget w)
It is called each time there is a repositioning. Perhaps that is overkill,
but no need to sweat this for now.
01 Mar 2012, RW Cox, 1dBport, level 2 (MINOR), type 2 (NEW_OPT)
Several things to keep Rick happy
Option '-band fbot ftop' can now be used more than once.
New option '-nozero' means to NOT include the 0 frequency.
New option '-invert' means to calculate the frequency indexes to remove
from the various '-band' options, then invert them to KEEP only those
frequencies instead. That is, only the frequencies NOT specified via
'-band' will be output in the resultant 1D file.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added option to use html viewer for WAMI results.
This is to allow users to click on a URL if one is available for a certain
atlas result. For now the display is very crude and only accessible with
-DWEBBY_WAMI=YES.
29 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'ctrl+W' that allows saving results from interactive correlations.
This allows for convenient saving of interactively created datasets
such as those from single-subject, or group correlation maps in resting
state.
27 Feb 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allow on the fly definition of standard meshes with -i ld120, for example.
27 Feb 2012, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in read_niml_file() that incorrectly set a read_header_only flag
27 Feb 2012, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
made a little more intelligent, e.g. make one backup by default
Note: can run this without any existing AFNI binaries, e.g.
@update.afni.binaries -bindir ~/abin -package linux_openmotif
27 Feb 2012, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Bug in combination of multiple affine transformations
Computation error in combining affine transformations
in whereami. Note all default transformations in whereami
do not combine affine transformations. Instead, space
transformations between TLRC and MNI_ANAT spaces are
computed using a 12-piece or a Brett transformation combined
with an affine in two stages.
24 Feb 2012, ZS Saad, general, level 3 (MAJOR), type 5 (MODIFY)
I/O library for R now can use AFNI's c library.
This new functionality allows the use a variety of formats
both surface and volume-based for reading to and writing from R.
3dMEMA can use this new functionality with option -cio
24 Feb 2012, ZS Saad, @RetinoProc, level 2 (MINOR), type 4 (BUG_FIX)
Added number of volume registration regressors to -ort_adjust
24 Feb 2012, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Options -val_diff and -sval_diff to compare values in 2 dsets.
24 Feb 2012, ZS Saad, 3dMEMA, level 2 (MINOR), type 2 (NEW_OPT)
3dMEMA can now handle surface-based data
It makes use of the new I/O functions that use AFNI's
C-library.
24 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
added -moderate_mask, fixed -extreme_mask help
Thanks to R Kuplicki for reporting the help inconsistency.
23 Feb 2012, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Enable 'bigthree' mode for color pbar
If AFNI_PBAR_THREE is YES, the color pbar in the AFNI GUI (but not the
renderer) will start in 'bigthree' mode, with 3 panes -- the colorscale
in the middle one, and the upper and lower panes adjustable to allow for
scaling that is not symmetrical.
22 Feb 2012, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Compute the mode of ROI voxels, see -mode and -nzmode
22 Feb 2012, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
moved GLOBAL_browser def from afni.h to thd_ttatlas_query.c
- declared in TTQ.h
- deleted #include thd_atlas.h from most .c files
- #include thd_atlas.h in mrilib.h
22 Feb 2012, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -randomize_trs and -seed
Affected 1d_tool.py, afni_util.py, lib_afni1D.py and lib_textdata.py.
21 Feb 2012, DR Glen, whereami, level 4 (SUPER), type 2 (NEW_OPT)
Web-based access atlases available
Able to query web atlases from whereami and open webpages
Support starting with rat brain atlas from Elsevier's
BrainNavigator
16 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
more quick termination updates
- added -max_images
- do not init vol search state to 2, would limit volumes to 40
- include fl_start in no_wait test
- look for new vol worth of images, but no volume match
14 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
release version 1.0: help, copy tables, scripts imply -no_gui
14 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if -no_wait, terminate on volume_match failure
For F Ye.
13 Feb 2012, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
-orig_vol now forces datum type to be same as that of input.
This fixed a problem with anatomicals ranging in the million(!) to
come up the equivalent of a binary mask with -orig_vol.
10 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Improved snapshot making. Previous bugs were caused by buffer swap problems
This fixed (I hope for good), problems of recording ('r'), continuous
recording (OS X and Linux), and the oversampling.
10 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
added 'paired' toggle box to GUI
09 Feb 2012, ZS Saad, 3dSurf2Vol, level 2 (MINOR), type 2 (NEW_OPT)
Added -sdata, making 3dSurf2Vol compatible with multitude of surface dsets
07 Feb 2012, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added -out option to handle output in various formats.
Also added -func ALL option.
07 Feb 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -bkg_col and -autorecord options
07 Feb 2012, ZS Saad, 3dcopy, level 2 (MINOR), type 4 (BUG_FIX)
Fixed problem with 3dcopy HHH.nii TTT+orig not producing output
Problem was caused by new change to EDIT_empty_copy() which
assigned storage mode to that of input dset instead of STORAGE_BY_BRICK
Fix involved setting storage mode per the prefix or view in
EDIT_dset_items()
06 Feb 2012, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added automatic sub-brick selection matching IxT in interface
Also see corresponding env var: SUMA_IxT_LinkMode
06 Feb 2012, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit was failing on the view change when target dset is under a path.
Problem was with default catenation of path to DSET_BRIKNAME and
DSET_HEADNAME. Those now contain the path automatically.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Improved (I hope) sub-brick labels. Added FDR too.
Same improvements to all 3dANOVA programs.
06 Feb 2012, ZS Saad, 3dANOVA3, level 2 (MINOR), type 4 (BUG_FIX)
Fixed compatibility with .niml.dset data
This required more improvements (I hope) to THD_init_diskptr_names() and
EDIT_empty_copy() for surface-based datasets.
06 Feb 2012, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
added -no_wait option: never wait for new data
Also, suppress new glob warnings.
Done for F Ye and others.
02 Feb 2012, RC Reynolds, uber_ttest.py, level 2 (MINOR), type 6 (ENHANCE)
added basic 3dMEMA capabilities
This affected afni_util.py, ask_me.py, gui_uber_ttest.py, lib_qt_gui.py
lib_subjects.py, lib_uber_ttest.py, uber_subject.py, uber_ttest.py.
01 Feb 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
check for pre-steady state outlier counts
Added option -tcat_outlier_warn_limit.
31 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
also update check for '### ASCCONV BEGIN' in to3d...
Problem noted by J Lewis.
31 Jan 2012, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for aligned anat _al_junk/keep
31 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_apply_ricor
30 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
ricor block: no longer apply in later 3dDeconvolve
The regressors for slice #0 from the ricor block were being applied in
the final regression (to remove motion) for consistency in degrees of
freedom. But we might rather not do that, particularly since DOF are
not important when proceeding with just correlation coefficients.
28 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
updates for surf analysis of subject FT under AFNI_data6
- added -atlas_followers to @SUMA_AlignToExperiment
- if surf analysis: no scaling mask (e.g. extents)
- updated help example #8 for surf analysis of AFNI_data6 subject FT
27 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fix inf loop if some sSliceArray entries not set
Also, now there might be junk between ASCCONV BEGIN and ###, grrrrr...
Problem noted by J Lewis.
26 Jan 2012, ZS Saad, 3dinfill, level 2 (MINOR), type 1 (NEW_PROG)
Fills holes in a volume based on neighboring values
This program is a wrapper to function SUMA_VolumeInFill.
Written in response to a query by Mike Beauchamp.
25 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
back out overzealous -quit changes for now
24 Jan 2012, ZS Saad, SurfExtrema, level 2 (MINOR), type 1 (NEW_PROG)
Finds nodes that are local extrema on the surface.
Program in response to request by Daniel Margulies
23 Jan 2012, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Allowed addition of 'R' or 'L' when jumping to a node.
This make DriveSuma work well with node indices that are specified
for two hemispheres as is done in the batch mode of 3dGroupInCorr.
This applies to both suma and DriveSuma
23 Jan 2012, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added -ld and -no_ld options
@SUMA_Make_Spec_FS by default now runs MapIcosahedron at two ld values.
23 Jan 2012, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -atlas_followers
Automatically bring along atlas datasets under -surf_anat's directory.
20 Jan 2012, RC Reynolds, to3d, level 2 (MINOR), type 5 (MODIFY)
mri_read_dicom: if there is no VALID vrCode, skip explicitVR
Done for Chad N.
19 Jan 2012, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Allow definition of DO on the fly with -fixed_do, -mobile_do.
See DriveAfni -help and suma -help_nido
19 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
made -quit more aggressive
18 Jan 2012, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT)
-s option to test string NI elements
18 Jan 2012, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 2 (NEW_OPT)
-closest_* options to create find nodes that fall closest to XYZ locations
18 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
force anat variable (and children) to be in AFNI format after 3dcopy
Appropriate, and for compatibility with an afni_name.pv change.
17 Jan 2012, ZS Saad, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Allowed BATCH mode to work on surfaces.
17 Jan 2012, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
-gert_create_dataset now implies -GERT_Reco and -quit
For Ziad and Daniel.
13 Jan 2012, ZS Saad, ParseName, level 2 (MINOR), type 2 (NEW_OPT)
Options -pre and -app help in creating filenames regarding of type
12 Jan 2012, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed ricor block 3dcalc loop for varying run lengths
11 Jan 2012, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
dx and dy were reversed in mri_read_dicom.c
Thanks to P Kaskan and F Ye for bringing this up.
10 Jan 2012, RW Cox, 1dBport, level 2 (MINOR), type 1 (NEW_PROG)
Generates sin/cos waveforms for bandpass-via-regression
04 Jan 2012, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Automatically add an Atlas to whereami list if encountered in the session
30 Dec 2011, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
NIFTI datasets used to loose their path information upon loading.
This is problematic for a few reasons. For instance, afni ~/tmp/joe.niml
will display the dataset as ./joe.niml. Some internal functions for
conveniently dealing with atlases fail when the path is messed up in this
way. Also, this problem occurred for NIFTI but NOT AFNI native formats
wich resulted in different behaviour for programs like 3drefit.
For example: 3drefit -space MNI ~/tmp/joe.nii is not comparable to
3drefit -space MNI ~/tmp/joe+tlrc. (Actually, that behaviour was patched
on Dec 27 but explicitly setting the path at output. But the fix needed
to happen for other programs so that is now done at the io level.)
30 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Simplified how afni handles custom group or single-subject atlases
By default, SessionAtlases and AFNI_SUPP_ATLAS_DIR/CustomAtlases.niml
are added to the atlas list for whereami queries.
30 Dec 2011, ZS Saad, @MakeLabelTable, level 2 (MINOR), type 2 (NEW_OPT)
Improved @MakeLabelTable's creation of ATLAS niml files
30 Dec 2011, ZS Saad, @Atlasize, level 2 (MINOR), type 1 (NEW_PROG)
A convenience script to turn a dataset to an atlas
The script makes it easy to create a group atlas or a single-subject
atlas and place them automatically in a location that AFNI
recognizes making them available to the user without bothering with
too many environment variable settings.
30 Dec 2011, ZS Saad, @AfniEnv, level 2 (MINOR), type 1 (NEW_PROG)
A convenience script to automatically edit .afnirc
30 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Numerous new options to 3dinfo, including checks for dset presence on disk
27 Dec 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
3drefit failed when refitting a NIFTI dset in another directory.
If you did something like 3drefit -space MNI joe/jim/dset.nii
you ended up with a new dataset ./dset.nii as opposed to modifying
the one under joe/jim/ directory
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA now allows for direct recording to disk.
See SUMA's ctrl+h for key ctrl+R for details.
Related environment variable is SUMA_AutoRecordPrefix.
20 Dec 2011, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA now displays area labels in the viewer, F9 key toggles it
See SUMA's ctrl+h output in the section for F9
Related environment variable is SUMA_ShowLabelsAtCrossHair.
20 Dec 2011, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
-prefix failed when input dset was mastered.
Better use macro PREP_LOADED_DSET_4_REWRITE whenever modifying
a dataset loaded from disk for the purporse of rewriting it.
20 Dec 2011, ZS Saad, 3dUpsample, level 2 (MINOR), type 2 (NEW_OPT)
Allow for upsampling to go to 11 (actually 320) and control output datum
13 Dec 2011, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
-init_xform to allow for an initial transformation of -surf_anat
13 Dec 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
-same_* options return information about dset pairs
12 Dec 2011, ZS Saad, apsearch, level 2 (MINOR), type 2 (NEW_OPT)
Small improvements and addition of logging option of search results
See -apsearch_log_file option for details. Logging is only enabled
if AFNI_LOG_BEST_PROG_OPTION is set to YES.
12 Dec 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Slice displays can now show atlas labels in addition to slice location
The displays are turned on by right-clicking on the slice viewer's color
bar and then setting the 'Label' to something other than 'OFF'
See isqCR_getlabel, ISQ_getlabel, and AFNI_get_dset_val_label in code
12 Dec 2011, ZS Saad, @global_parse, level 2 (MINOR), type 1 (NEW_PROG)
Script to simplify support of global options such as h_find from scripts
07 Dec 2011, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Added atlas creation of aseg, aparc+aseg, in addition to aparc.a200*
See whereami's example 3 for how to extract ROIs from FreeSurfer atlases.
02 Dec 2011, ZS Saad, ConvertSurface, level 2 (MINOR), type 2 (NEW_OPT)
-XYZscale is added to scale the coordinates of a surface
Surface that are not in mm coordinates can look pretty bad in SUMA.
This scaling option can be used to easily change coordinates from cm to mm
for example.
22 Nov 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
allow for passing variables directly, not via -svar
21 Nov 2011, RC Reynolds, quick.alpha.vals.py, level 2 (MINOR), type 1 (NEW_PROG)
a very simple program to tabulate the output from slow_surf_clustsim.py
This ought to be improved, but at least it is now distributed...
17 Nov 2011, ZS Saad, apsearch, level 2 (MINOR), type 1 (NEW_PROG)
This is a program to test approximate string matching functions
The program is best described by its help output.
It is meant to quickly test the behavior of the approx* functions
in thd_ttatlas_query.c where approximate string matching will
be useful is easily specifying an atlas areas by name.
Another useful offshoot is the function: suggest_best_prog_option
which can easily be called right after a command-line parsing error
message is displayed. For example, in apsearch I have the following:
{ /* bad news in tennis shoes */
fprintf(stderr,"** Error %s: bad option %s\n", argv[0], argv[iarg]);
suggest_best_prog_option(argv[0], argv[iarg]);
return 1;
}
So all is needed to retrofit an old program is the suggest function.
That function will do nothing if environment variable AFNI_NO_OPTION_HINT
is set.
To use suggest_best_prog_option from a script, use:
apsearch -popt `basnemane $0` -word ARG
17 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
If AFNI_NO_OPTION_HINT, don't bother with helpful suggestions
17 Nov 2011, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
if dset+orig is anat/func and dset+tlrc is func/anat, 'BAD dataset', man
Altered logic in thd_initsess.c (done with dglen).
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug introduced by cleaning up header_name and brick_name
15 Nov 2011, ZS Saad, afni_general, level 2 (MINOR), type 4 (BUG_FIX)
More changes regarding obliquity warnings.
AFNI:
Popups only appear when user is viewing dsets of different obliquity.
See dset_obliquity_angle_diff()
and THD_report_obliquity()
The warnings only appear ONCE per pair of misfits, per afni process.
See AFNI_check_obliquity() for implementation details.
Oblique notices no longer appear on the command line each time you
read a session or switch dsets. To tell you that you are viewing an
oblique dset and that the coords are not quite what they should be,
I added a '*' next to the 'order:' descriptor in the top left corner.
Command Line programs:
In most programs that should not care about obliquity, I add
early under main():
set_obliquity_report(0); /* silence obliquity */
Also, 3dcalc, 3dTcat, 3dbucket, and function THD_open_tcat()
Only complain when obliquity between dset pair differs.
The check is done right after checking for grid matching with
EQUIV_DATAXES
15 Nov 2011, RW Cox, dicom_hinfo, level 2 (MINOR), type 1 (NEW_PROG)
For printing out info from lots of DICOM files
For each file input, prints 1 line with the values of only the desired
tags. The goal is to be helpful in figuring out which files go
together. See Example #2 in the help output for such a case.
10 Nov 2011, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Turned off obliquity popup warning when Ulay and Olay angles are similar
AFNI issues warning when obliquity differs for a pair of viewed sets.
It does not repeat warnings for a certain pair. It only output one set
of warnings per dataset when 'switch ulay' is set, although I'd love to
get rid of that habit as soon as possible.
10 Nov 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add ExtraSet option
That is, to correlate seeds from the TimeSeries dataset with voxel data
from the ExtraSet dataset. Ziad asked for something like this, so here
it is.
09 Nov 2011, RW Cox, 3dUndump, level 2 (MINOR), type 2 (NEW_OPT)
Add -ROImask option
To put values into locations defined by a mask dataset.
09 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
-surf_blur_fwhm is no longer valid, please use -blur_size
07 Nov 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
No -iresp or -sresp for dmBLOCK
Also, change definition of 'near-duplicate' times from 0.05*TR to 0.50*TR
07 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -blur_to_fwhm and -blur_opts_B2FW
Added for E Nelson and J Jarcho.
07 Nov 2011, DR Glen, lost last character in sub-brick labels, level 2 (MINOR), type 4 (BUG_FIX)
Fixed miscount of characters
07 Nov 2011, DR Glen, deobliquing, level 2 (MINOR), type 5 (MODIFY)
More programs lose original data obliquity
3drefit, 3dWarp, 3daxialize, 3dZcutup, 3dCM, 3dZregrid
added to the list of programs
04 Nov 2011, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 6 (ENHANCE)
added 'mode' mapping function
Requested by R Mruczek. Also done for Z Puckett.
03 Nov 2011, RC Reynolds, @2dwarper.Allin, level 2 (MINOR), type 2 (NEW_OPT)
added -prefix option; allow for 3dAllin failures; copy time info
Updates by N Mei and A Messinger.
03 Nov 2011, DR Glen, longer sub-brick labels, level 2 (MINOR), type 5 (MODIFY)
Allow sub-brick labels to be up to 63 characters
03 Nov 2011, DR Glen, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Allow refitting of some attributes
Some attributes like IJK_TO_DICOM_REAL and DELTA were not
being updated correctly with the original values remaining
in the dataset
02 Nov 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added out.TENT_warn.txt to warning file review
02 Nov 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if using TENT, run 'timing_tool.py -warn_tr_stats'
Warnings are also saved in out.TENT_warn.txt.
02 Nov 2011, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
allow -save_file_list to apply even with -infile_list
31 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_tr_stats and -warn_tr_stats options
25 Oct 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
process married files with current operations
1. AfniMarriedTiming inherits from AfniData (instead of local copies)
2. add all AfniTiming methods to AfniMarriedTiming (as married timing)
3. rename AfniMarriedTiming back to AfniTiming (but now married)
25 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
look for more file name variants, including with '_' separators
Added for J Weisberg.
20 Oct 2011, RC Reynolds, afni_general, level 2 (MINOR), type 5 (MODIFY)
changed most resampling programs to deoblique inputs upon read
THD_open*_dataset() was followed by THD_make_cardinal().
modified: 3dresample, 3dfractionize, 3drotate, adwarp, 3dLRflip
3dZeropad, 3dZcat, 3dAutobox
not (yet) modified: 3dWarp(Drive), 3dAllineate
19 Oct 2011, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
can read/write ascii COMPLEX64, COMPLEX128, RGB24
Requested by H Breman, J Mulders and N Schmansky.
18 Oct 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
added blur size control; removed requirement of stim timing files
14 Oct 2011, ZS Saad, afni-general, level 2 (MINOR), type 0 (GENERAL)
Improvements of atlas handling in whereami and afni
1- In addition to loading atlas specs from environment variable
AFNI_SUPP_ATLAS, AFNI will automatically search for a file
named SessionAtlases.niml which is created with @MakeLabelTable.
2- AFNI will check if a viewed dataset is an atlas and will
automatically add it to the atlas list. It will also show the label at
the cross-hair location.
New functions of interest:
get_Atlas_ByDsetID, is_Dset_Atlasy,
label_table_to_atlas_point_list, is_identity_xform_chain
14 Oct 2011, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
now processes surface data
- added 'surf' processing block, and corresponding '-surf_*' options:
-surf_anat, -surf_spec, -surf_anat_aligned, -surf_anat_has_skull,
-surf_A, -surf_B, -surf_blur_fwhm
- compute errts and TSNR by default (had required option or blur est)
14 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
allow modest handling of surface results
13 Oct 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
-omask failed if atlas was stored in float type.
13 Oct 2011, ZS Saad, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
Added support for -atrstring operation on NIFTI datasets
This required making changes to THD_init_diskptr_names functions
and a few more of its colleagues.
13 Oct 2011, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fixed error in computing with un-centered covariates
inv[Xt*X] matrix not computed correctly in mri_matrix_psinv_pair()
function.
11 Oct 2011, ZS Saad, @auto_tlrc, level 2 (MINOR), type 2 (NEW_OPT)
Added support for NIFTI datasets
11 Oct 2011, ZS Saad, 3dinfo, level 2 (MINOR), type 2 (NEW_OPT)
Added new options for extracting field values in scripts
04 Oct 2011, ZS Saad, GroupAna, level 2 (MINOR), type 2 (NEW_OPT)
Added support for writing NIML files as output
This also required writing a few new matlab functions such as
BrikInfo_2_niml_writesimple.
04 Oct 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
changed basic script outputs
- added 'max censored displacement', 'final anat dset' and
'final voxel resolution' to basic script
- removed 'num stim files found'
03 Oct 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_infile (e.g. to remove TRs from motion params)
Added for N Adleman.
22 Sep 2011, RC Reynolds, uber_ttest.py, level 3 (MAJOR), type 1 (NEW_PROG)
a graphical program for running either 3dttest++ or 3dMEMA
Still under destruction.
22 Sep 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
altered spacing and made other minor changes
22 Sep 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
added check_for_file and for_dset, updated find_x_mat, enorm, view_stats
22 Sep 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
various updates
- updated quotize_list
- added nuke_final_whitespace, flist_to_table_pieces, get_ids_from_dsets
13 Sep 2011, DR Glen, 3dMean, level 2 (MINOR), type 2 (NEW_OPT)
Added non_zero and count options
06 Sep 2011, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
save_skullstrip option saved obliqued and skullstripped data
Fixed to save only skullstripped
02 Sep 2011, DR Glen, 3dhistog, level 2 (MINOR), type 4 (BUG_FIX)
Handle binning and output of integer and float data differently
Distinguish between integer and float data. Added float and int
options to enforce specified behavior.
Done with Rick Reynolds.
01 Sep 2011, RC Reynolds, @radial_correlate, level 2 (MINOR), type 1 (NEW_PROG)
compute voxelwise EPI correlations with local spherical averages
30 Aug 2011, DR Glen, Draw Dataset, level 2 (MINOR), type 4 (BUG_FIX)
Draw Dataset plugin incorrect label for current atlas
Fixed current atlas to be updated properly if atlas is
changed.
19 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 5 (MODIFY)
Fix &readpoly() and implement &read4x4()
Modify 3dNwarpApply to use same function as &apply() so that the 2
programs are in sync.
Release 3dNwarpCalc into the wild:
Born free, and code is worth running, but only worth running, because
you're born freeware!
19 Aug 2011, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D sresp datasets
Requested by S Baum.
09 Aug 2011, RW Cox, 3dNwarpCalc, level 2 (MINOR), type 1 (NEW_PROG)
Implemented about 80% of it
Seems to work, but needs a fair amount of fine tuning and testing.
03 Aug 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
changed aea.py -save_skullstrip to -save_orig_skullstrip
The -save_skullstrip dataset might have an oblique transformation
applied (which would throw off EPI if it is then sent to standard
space). Apply the new option to grab a simple skull-stripped anat.
Thanks to A Ellenstein for reporting it and Z Saad for help understanding.
02 Aug 2011, RW Cox, 3dclust, level 2 (MINOR), type 2 (NEW_OPT)
Add '-inmask' option, to use internal mask
To be compatible with AFNI's Clusterize GUI, which was also modified to
output this option when appropriate.
01 Aug 2011, ZS Saad, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Whereami's symbolic notation failed with float valued atlases
This is now fixed. Code also checks for scale factors.
There was another bug waiting to happen with:
!is_Atlas_Named(atlas, "CA_N27_PM"), which is now:
!is_probabilistic_atlas(atlas)
01 Aug 2011, ZS Saad, Draw Dataset, level 2 (MINOR), type 5 (MODIFY)
Changed the gap selection to arrows to allow for much larger gaps
29 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
z.max files are now named by p-value
And suggest a quick.alpha.vals.py command.
29 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 5 (MODIFY)
changes to handle python 2.4, where shell output has extra blank lines
29 Jul 2011, RC Reynolds, 3dUniformize, level 2 (MINOR), type 4 (BUG_FIX)
fixed checks against lower_limit in option processing (since -1 init)
Thanks to A Waite for reporting the problem and cause in the code.
26 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if e2a, update current anat to skull-stripped anat from align block
This would avoid a second skull-strip step in @auto_tlrc.
25 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 6 (ENHANCE)
added keepblocks var, to limit kept intermediate datasets
22 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 4 (BUG_FIX)
after blur, rescale noise to be normally distributed
21 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 5 (MODIFY)
changed TR counts to come via awk instead of grep
20 Jul 2011, RC Reynolds, make_pq_script.py, level 2 (MINOR), type 1 (NEW_PROG)
program will generate a script to produce a p-value/q-value curve pair
14 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 6 (ENHANCE)
added 'max motion displacement' to basic script
14 Jul 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_max_displace, for maximum motion displacement
13 Jul 2011, RW Cox, 3dTcorrMap, level 2 (MINOR), type 4 (BUG_FIX)
Bug in computation of indx
The mask is turned into an index table of active voxel indx[]. However,
constant voxels were removed from the mask AFTER indx[] was created,
which is stupid. This is fixed now, and Zhark will be chastised.
13 Jul 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
run gen_ss_review_scripts.py and any resulting 'basic' review script
11 Jul 2011, RC Reynolds, gen_ss_review_scripts.py, level 3 (MAJOR), type 1 (NEW_PROG)
for generating single subject review scripts
To be run by the afni_proc.py proc script or directly by users.
11 Jul 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed case of partial path match to dsets
Problem found by J Jarcho.
11 Jul 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ATLAS_COLORS and default atlas in AFNI GUI
Set atlas to use for Atlas colors, Go to atlas location,
Draw Dataset and Renderer. Name of atlas can be set in
environment and modified in the AFNI GUI environmentalism menu.
Several other environmental variables regarding atlas usage
can also be modified there too.
08 Jul 2011, RC Reynolds, slow_surf_clustsim.py, level 2 (MINOR), type 5 (MODIFY)
added -on_surface, which might not end up being so useful
05 Jul 2011, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
minor enhancements to 5 python files (prep for gen_ss_review_scripts.py)
01 Jul 2011, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Replace text-only AFNI Tips with HTML-based
Allows incorporation of images and better formatting.
Uses XmHTML widget set, whose source code is also added to AFNI.
27 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
added -dset_index0_list/-dset_index1_list options, etc.
- ttest++ and MEMA commands now apply directories to datasets
- changed Subject.atrs to be VarsObject instance, not dictionary
27 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WHEREAMI_DEC_PLACES
Set precision for whereami output
Higher field data and animal atlases require higher precision.
The default value used for focus point among template spaces is
still 0 decimal places (closest mm), but animal data requires three
decimal places. Value may range from 0 to 10.
24 Jun 2011, RC Reynolds, slow_surf_clustsim.py, level 3 (MAJOR), type 1 (NEW_PROG)
a temporary program until we do this in C
23 Jun 2011, RW Cox, afni InstaCorr, level 2 (MINOR), type 5 (MODIFY)
Ability to INIT-ialize InstaCorr from a plugout
Details are in README.driver, under the INSTACORR command section.
23 Jun 2011, DR Glen, whereami, level 2 (MINOR), type 3 (NEW_ENV)
Desai MPM atlases
New maximum probability map atlases derived from the Desai probability
maps just introduced in distribution.
20 Jun 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added eta2 function (alongside '3ddot -doeta2')
16 Jun 2011, ZS Saad, 3dSurfMask, level 3 (MAJOR), type 2 (NEW_OPT)
Major improvements for mask creation and voxel distance computations
Option -fill_method SLOW produces more accurate masks for voxels
inside the closed surface. In addition, the program outputs a dataset
with the shortest distance of each voxel to the surface.
See examples under 3dSurfMask -help.
16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
-flip_orientation allows for reversing triangle orientation.
See new examples under SurfPatch -help
16 Jun 2011, ZS Saad, SurfPatch, level 2 (MINOR), type 4 (BUG_FIX)
No longer complains about not finding seed in cases where it should.
16 Jun 2011, RC Reynolds, 3ddot, level 2 (MINOR), type 2 (NEW_OPT)
added -doeta2 via new THD_eta_squared_masked
Added for Shinchan.
15 Jun 2011, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 6 (ENHANCE)
if constant dset names, extract SIDs from dir names
Done for R Momenan.
10 Jun 2011, DR Glen, whereami, level 4 (SUPER), type 0 (GENERAL)
Generic Atlas Support and new atlases
Atlases, spaces and transformations are now defined in a NIML file,
AFNI_atlas_spaces.niml. Transformations among spaces for coordinates
are defined in that file for use by whereami and the whereami display
in the AFNI GUI. The flexible naming of the spaces and atlases allows
easy addition of new atlases to AFNI processing.
Two new environment variables control what atlases and spaces are shown
when no atlas is specified, AFNI_ATLAS_LIST and AFNI_TEMPLATE_SPACE_LIST
The list of atlases now defaults to the TT_Daemon and the Eickhoff-
Zilles atlases in MNI_ANAT space.
Additionally, the cytoarchitectonic atlases from the Zilles, Eickhoff
group have been updated to the most recent version, 1.8.
***The previous versions, 1.5, are not used in this release by default.
Depending upon differences on how regions or codes are defined and used,
it is possible that processing scripts and results may be affected.
With this release, we also introduce three probabilistic atlases
donated by the Desai group generated from a typical AFNI pipeline.
These atlases contain a multitude of regions created using both
@auto_tlrc and FreeSurfer.
08 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT)
Added -npb and modified title bar to reflect bloc of ports
You can have multiple instances of programs talking to each other.
See afni's help for details on the -npb option.
08 Jun 2011, ZS Saad, @FSlabel2dset, level 2 (MINOR), type 1 (NEW_PROG)
Script to change FreeSurfer ascii label file to SUMA dset
07 Jun 2011, ZS Saad, afni-general, level 3 (MAJOR), type 2 (NEW_OPT)
Allow multiple instances of communicating programs per machine.
This was done by generalizing option -np PORT_OFFSET which
allows users to use a different set of ports for different AFNI/SUMA/etc.
sessions.Port numbers should no longer be hard coded anywhere. New dedicat
ed
ports should be added to then new init_ports_list() function.
07 Jun 2011, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added 'w' key for writing out colormap to disk.
See suma's help for the colormap.
(press ctrl+h with cursor over the colormap in the surface controller)
03 Jun 2011, RC Reynolds, Makefile, level 2 (MINOR), type 2 (NEW_OPT)
removed -lpng from Makefile.macosx_10.6_Intel_64
We added -lpng because we were compiling our own OpenMotif
(configure option?), but fink's version does not need it.
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
compute TSNR datasets (added -compute_tsnr); added -regress_make_cbucket
02 Jun 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
de-meaned motion regressors is now the default
- added -regress_apply_mot_types to specify motion types for regression
- added -regress_no_motion_demean and -regress_no_motion_deriv
- by default, demean and deriv motion parameters are created
- by default, demean motion parameters are applied in the regression
(replacing the original 'basic' parameters, which should have no
change in betas of interest, just the constant polort betas)
27 May 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
re-work of motion, as prep for more motion options
- replaced -volreg_regress_per_run with -regress_motion_per_run
- made uniq_list_as_dsets() a warning, not an error (for J Britton)
27 May 2011, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -split_into_pad_runs (for regress motion per run)
25 May 2011, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
Fix problem with TENT and CSPLIN
For non-integer TR, could miss evaluating the last function in a TENT or
CSPLIN series because of roundoff error pushing the evaluation time
slightly past the 'top' value. This is bad if the function is 1 at
exactly this value, as the last functions are here. Solution was to
change the test to allow evaluation at values slightly larger than
'top'.
25 May 2011, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -global_to_local and -local_to_global for G Chen
24 May 2011, RC Reynolds, 1dplot, level 2 (MINOR), type 4 (BUG_FIX)
fixed plotting of varying length time series
20 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 2 (NEW_OPT)
Add normal theory CI for Pearson; Add -block option
Pearson correlation (the default) now gets the normal theory confidence
interval printed at no extra charge.
To allow for serial correlation, the -block option enables random length
block resampling bootstrap.
Add some more help text to explicate things a little better.
20 May 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
execute via /usr/bin/env python
Help now suggests fink as primary Mac source for PyQt4.
20 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 5 (MODIFY)
execute via /usr/bin/env python
19 May 2011, ZS Saad, @RetinoProc, level 2 (MINOR), type 2 (NEW_OPT)
Added support for multiple reference time series.
Search for -var* options in @RetinoProc -help.
19 May 2011, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 2 (NEW_OPT)
Added option to use best of multiple reference time series.
Search for -multi_ref_ts in 3dRetinoPhase -help
19 May 2011, RW Cox, 1dCorrelate, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation coefficients of 1D columns
Pearson, Spearman, Quadrant, or Kendall tau_b.
Main goal is to provide the bias-corrected bootstrap estimate of the 95%
confidence interval.
18 May 2011, ZS Saad, @RetinoProc, level 3 (MAJOR), type 2 (NEW_OPT)
Added options for mapping to specific layers, and the use of delay
The options -wm, -pial, etc. allow for tight control of mapping
onto specific layers in the cortex.
Option -delay improves latency estimation compare to using the phase
of the fundamental frequency.
18 May 2011, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 2 (NEW_OPT)
Added options to 3dRetinoPhase to estimate latency as in 3ddelay
The two options for computing delays, instead of phase, are
-phase_estimate DELAY, and -ref_ts REF_TS . See program's -help for
details.
Also added -ort_adjust which is needed to account for lost DOF in
external detrending when estimating the significance of correlation
coefficients with delay estimation.
The program now output a correlation coefficient with the visual field
angles datasets.
And speaking of correlation coefficients, the significance levels should
be taken with a grain of salt, especially in derived datasets such as
field angle, and VFR in SurfRetinoMap.
18 May 2011, ZS Saad, SurfRetinoMap, level 2 (MINOR), type 5 (MODIFY)
Added a correlation coefficient with VFR output.
18 May 2011, ZS Saad, 3ddelay, level 2 (MINOR), type 2 (NEW_OPT)
Added options to 3ddelay to improve its utility for retinotopy analysis
The new options are -phzreverse and -phzscale. Though useful, you are
better off using 3dRetinoPhase -phase_estimate DELAY option. It is much
more convenient for retinotopy analysis and fits better in @RetinoProc
16 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
could be used as a release version
- added 'check center dist' button, to display the current distance
- added menu item to show afni command for viewing results
- added menu items to show python and shell command windows
- added much more help, including main and section buttons
- added browsing of align_epi_anat.py help
13 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
added working GUI (for options, GUI help still needs ... help)
12 May 2011, RC Reynolds, uber_skel.py, level 3 (MAJOR), type 1 (NEW_PROG)
A working skeleton for future uber programs.
This is based on uber_align_test.py, version 0.2.
12 May 2011, RC Reynolds, uber_align_test.py, level 2 (MINOR), type 6 (ENHANCE)
many small updates
This set of 3 files was broken off set uber_skel.py, meant to be a
reasonable starting point for future uber programs.
11 May 2011, RC Reynolds, uber_align_test.py, level 3 (MAJOR), type 6 (ENHANCE)
added basic graphical interface, still need to add variable fields
o also made single cost_list
o also added -help_howto_program, which might move to a skeleton program
02 May 2011, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
added nul-termination and a.b[.d]+ rules for checking Siemens slice times
Problem noted by D Kravitz and S Lee.
28 Apr 2011, RC Reynolds, uber_align_test.py, level 3 (MAJOR), type 1 (NEW_PROG)
for testing EPI/anat alignment with various align_epi_anat.py options
This is a command-line version, with a GUI to come soon.
28 Apr 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 2 (NEW_OPT)
reconcile LUS.py with LS.py in prep for uber_align_test.py
28 Apr 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -align_epi_strip_method
25 Apr 2011, ZS Saad, afni-general, level 3 (MAJOR), type 5 (MODIFY)
Major reorganization of 'whereami' functionality.
The code changes affect anything related to atlas datasets and whereami
functionality. The changes were made take advantage of Daniel Glen's new
API to handle atlas, space, and template definitions.
There is now very little reliance on hard coded atlas information in the
source code. Whatever is left is needed to ensure backward compatibility.
25 Apr 2011, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
have Dimon send 'TPATTERN explicit' with slice timing to RT plugin
25 Apr 2011, RC Reynolds, Imon, level 2 (MINOR), type 5 (MODIFY)
Imon is getting phased out of the distribution (see 'Dimon -use_imon')
Requires compiling alterations to be put back in (if anyone wants it).
24 Apr 2011, RC Reynolds, @Align_Centers, level 2 (MINOR), type 6 (ENHANCE)
allow -base dset to be in PATH, AFNI_PLUGINPATH, etc.
22 Apr 2011, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
if manual tlrc and -volreg_tlrc_adwarp, also transform extents mask
Noted by J Britton.
Also, if -regress_reml_exec, insert 3dClustSim table in stats_REML.
Noted by R Momenan.
15 Apr 2011, RC Reynolds, dicom_hdr, level 2 (MINOR), type 2 (NEW_OPT)
added -slice_times and -slice_times_verb, to show siemens slice timing
15 Apr 2011, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
added FROM_IMAGE as default Siemens slice pattern in to3d command
13 Apr 2011, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added FROM_IMAGE timing pattern (for Siemens mosaic images)
08 Apr 2011, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Added options -reduce* to compute results on reduced grid
This would help in speeding up the computing of stats over large regions
without paying too high a premium on processor time.
Changes were made in 3dLocalstat.c and mri_nstats.c.
Micro modification in r_new_resam.c's r_new_resam_dset.
07 Apr 2011, DR Glen, whereami, level 3 (MAJOR), type 3 (NEW_ENV)
Framework changes for generic atlases
Atlases now can have segmentation in a NIML structure attribute
in the atlas dataset header. The environment variable,
AFNI_CUSTOM_ATLAS, can contain a custom atlas prefix. Details on
NIML attributes will be forthcoming. In the meantime, existing
atlases should work as before with the minor exception of mask
datasets are now set to have voxel values of 1 rather than
the values from the atlas dataset.
05 Apr 2011, RC Reynolds, howto, level 2 (MINOR), type 6 (ENHANCE)
updated the class setup and basic Linux instructions for PyQt4
29 Mar 2011, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug in default view of flat surfaces.
The problem manifested itself when large rotations were present
in the transform of the sv volume, resulting in flat meshes
being incorrectly labeled as spherical.
29 Mar 2011, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Basic support for HTTP/1.1
See functions read_URL_http11, and page_* in thd_http.c.
29 Mar 2011, ZS Saad, ConvexHull, level 2 (MINOR), type 4 (BUG_FIX)
Fixed error with proj_xy option.
24 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
added align and tlrc option boxes, adjusted spacing
24 Mar 2011, DR Glen, whereami, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug for case of MNI_ANAT space as not processed
23 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
moved gltsym box to below stim, save AP output, small mac install update
22 Mar 2011, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT)
-roi_mask allows creation of separate histogram for each ROI in mask.
22 Mar 2011, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
nwarp_pass != nwarp_type :-(
Causing bug in application of nonlinear warps from external files.
22 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
processing status, clear options/fields menu items, etc...
22 Mar 2011, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
mri_read_dicom: if there is no vrCode, skip explicitVR
21 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
many updates, including extra regress options box
20 Mar 2011, RC Reynolds, uber_subject.py, level 3 (MAJOR), type 6 (ENHANCE)
handle symbolic GLTs, etc.
19 Mar 2011, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug for case master_dset2_dxyz was accidentally ignored
14 Mar 2011, DR Glen, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bugs when switching between ROI and continuous overlay datasets
Colorscale (scale, range) is restored with continuous overlay dataset.
Need to set AFNI_INT_CMAP or AFNI_INT_PBAR to use.
14 Mar 2011, DR Glen, Draw Dataset Plugin, level 2 (MINOR), type 5 (MODIFY)
Update Draw Dataset for clarity and ROI labels
Draw Dataset is clearer with regards to overlay/underlay drawing
instead of the older func/anat terminology. Also an ROI color scale
is used for drawing and labels are updated in the AFNI Overlay GUI
immediately. Need to set AFNI_INT_CMAP or AFNI_INT_PBAR to use.
08 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
uber_subject.py command menu item, ...
07 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
updates: command and pycommand windows, new Process classes, ...
04 Mar 2011, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug with 1-sample results in -paired run
Forgot to turn off the 'paired' opcode for the 1-sample (no covariates)
analyses, so results were all zero!
03 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
updates: control vars, subj dir, view actions, result vars, ...
02 Mar 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 6 (ENHANCE)
many updates, including write and exec of proc script
There is still much to do before first release version.
28 Feb 2011, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Clusterize: add scatterplot ('S:') options
For Rasmus
22 Feb 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
added interfaces for 'expected' option
16 Feb 2011, RC Reynolds, uber_subject.py, level 2 (MINOR), type 5 (MODIFY)
epi or stim list from command line can init order/labels; file reorg
Also, initiated regression testing tree.
16 Feb 2011, RC Reynolds, howto, level 2 (MINOR), type 5 (MODIFY)
updated the main page and basic Linux instructions
15 Feb 2011, RC Reynolds, uber_subject.py, level 4 (SUPER), type 1 (NEW_PROG)
added CLI (command-line interface), generates basic afni_proc.py script
Many enhancements yet to come.
14 Feb 2011, RC Reynolds, uber_proc.py, level 2 (MINOR), type 0 (GENERAL)
moved uber program into main repository
12 Feb 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
updates for uber_subject.py
07 Feb 2011, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Added -batch mode of operation
To appease the Lebanese and Italian masses.
01 Feb 2011, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
updates for parsing a stim file list
27 Jan 2011, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 2 (NEW_OPT)
Add -sendall option, to palliate the Texan hordes.
20 Jan 2011, RW Cox, 3dClustSim, level 2 (MINOR), type 4 (BUG_FIX)
Small ROI masks could give weird and wrong results
Problem was when a desired alpha level (say 0.10) simply couldn't be
found -- e.g., only 6% of simulations had ANY above-threshold voxels in
the mask. Bad-ositiness ensued since the program didn't check for this
case. Now it checks, uses N=1 as the result in such cases, and
stderr-ifies a warning message also.
The problem with developing software is users. If we didn't have them,
life would be much easier.
19 Jan 2011, RC Reynolds, lib_subjects.py, level 2 (MINOR), type 6 (ENHANCE)
many updates to the VarsObject class
13 Jan 2011, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -gert_write_as_nifti and -gert_create_dataset
requested by V Roopchansingh
04 Jan 2011, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
Fixed SurfSmooth to work with the combination HEAT07+Sparse Dsets+cmask
The problem was caused by a bad masking operation at the detrending
function when sparse datasets with cmask option are used. The detrending
is used to estimate the FWHM in the blurmaster. As a result, SurfSmooth
would not converge under such circumstances.
In addition there was an optimizer related bug in the macro SUMA_COL_FILL
Thanks to Christopher Ackerman from JHMI for reporting the bug.
04 Jan 2011, ZS Saad, SurfFWHM, level 2 (MINOR), type 4 (BUG_FIX)
Fixed SurfFWHM which had the same masking problem as SurfSmooth.
04 Jan 2011, RC Reynolds, Dimon, level 3 (MAJOR), type 6 (ENHANCE)
version 3.0 : handle Siemens Mosaic formatted files
- depend on libmri, return MRI_IMARR from mri_read_dicom, changes
for oblique and mosaic processing
- mri_read_dicom.c: g_info (process control), g_image_info (Dimon)
replaced DEBUG_ON/debugprint with g_info.verb, many small changes
- mri_dicom_elist.h: merged with dimon_afni.h
- mcw_glob.[ch]: control sort direction via rglob_set_sort_dir()
03 Jan 2011, ZS Saad, 3dUniformize, level 2 (MINOR), type 2 (NEW_OPT)
Changed 3dUniformize to accept byte, short, or float input.
These changes also avoid data clipping that was necessary
when output data was handled as shorts.
The output format is similar to that of the input.
-auto_clip is now the default.
30 Dec 2010, RW Cox, 3dApplyNwarp, level 2 (MINOR), type 1 (NEW_PROG)
Applies -nwarp_save output from 3dAllineate
Lets you apply a 3D nonlinear deformation to another file. Works OK,
but changes will come.
23 Dec 2010, RW Cox, 3dPolyfit, level 2 (MINOR), type 1 (NEW_PROG)
Fits a polynomial (spatially) to a dataset
23 Dec 2010, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -use_old_mosaic_code
This is phase 1 of dealing with Siemens mosaic format in Dimon.
Siemens mosaic functions we moved to new mri_process_siemens.c,
with the ability to use the old code preserved with this option.
21 Dec 2010, ZS Saad, @help.AFNI, level 2 (MINOR), type 1 (NEW_PROG)
A simple script to look at AFNI's all help page
16 Dec 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
updates to file type (looks like) errors and warnings
16 Dec 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
updates to file type (looks like) errors and warnings
15 Dec 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
use lib_textdata.py for reading timing files, allow empty file
empty file update for C Deveney
14 Dec 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problem with timing file tests on 'empty' files with '*'
problem noted by C Deveney and R Momenan
10 Dec 2010, ZS Saad, 3BrickStat, level 2 (MINOR), type 2 (NEW_OPT)
Added -mrange and -mvalue options to 3dBrickStat
09 Dec 2010, ZS Saad, 3dhistog, level 2 (MINOR), type 2 (NEW_OPT)
Made 3dhistog output NIML 1D format with -prefix option
With -prefix's output users can get properly labeled
output with a simple command like 1dRplot -input hist.1D
08 Dec 2010, RW Cox, 3dXYZcat, level 2 (MINOR), type 1 (NEW_PROG)
Generalized 3dZcat.
No generalized 3dZcutup yet, though.
06 Dec 2010, RW Cox, @2dwarper, level 2 (MINOR), type 0 (GENERAL)
Modify script to deal with non-axial slices
30 Nov 2010, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added option -final_sort_by_prog
22 Nov 2010, ZS Saad, 3dRowFillin, level 2 (MINOR), type 2 (NEW_OPT)
Added XYZ.OR, and XYZ.AND to 3dRowFillin
19 Nov 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -write_all_rest_times, moved write_to_timing_file to afni_util.py
option added for J Poore
16 Nov 2010, ZS Saad, ExamineXmat, level 2 (MINOR), type 2 (NEW_OPT)
A major rewrite of ExamineXmat
see ExamineXmat -help for details
10 Nov 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add -rankize and -no1sam options
08 Nov 2010, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 2 (NEW_OPT)
can now generate 3dttest++ commands
05 Nov 2010, ZS Saad, 3dkmeans, level 3 (MAJOR), type 1 (NEW_PROG)
3dkmeans is a program for performing kmeans clustering
Program was written by A. Vovk and Z. Saad, based on
The C clustering library.
Copyright (C) 2002 Michiel Jan Laurens de Hoon.
See suma -sources for copyright details
See 3dkmeans -help for usage details.
05 Nov 2010, ZS Saad, niccc, level 2 (MINOR), type 2 (NEW_OPT)
Added -attribute, -match, and -f options to niccc
See niccc -help for details.
05 Nov 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
New -BminusA option
This is Ziad's fault (again).
04 Nov 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added regress_basis_multi, -regress_no_ideal_sum
One can specify either one basis function or one per stim_times file.
02 Nov 2010, RC Reynolds, 3dTstat, level 2 (MINOR), type 6 (ENHANCE)
allow single volume input for functions mean, max, min, sum
Other functions can be added to this list as needed.
01 Nov 2010, ZS Saad, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
3dBrickStat's percentile option did not work with byte datasets
29 Oct 2010, ZS Saad, @ElectroGrid, level 2 (MINOR), type 1 (NEW_PROG)
A script for facilitating ECOG grid creation
29 Oct 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_indices_baseline, _motion and _interest
28 Oct 2010, ZS Saad, @RegroupLabels, level 2 (MINOR), type 1 (NEW_PROG)
A script for regrouping label datasets
27 Oct 2010, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -show_bad_char and -show_bad_all
26 Oct 2010, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
solidified 3dMEMA commands
This is now used to generate AFNI_data6/group_results/s4.3dMEMA.V-A.
25 Oct 2010, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 1 (NEW_PROG)
a program to generate group commands (3dMEMA for now)
Commands to come: 3dttest(++), 3dANOVA*, GroupANA.
22 Oct 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed rendering of spheres, which were affected by ambient light.
Thanks to MSB for the complaint.
22 Oct 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added NodeMarker field to the spec file
The NodeMarker is a NIDO object that gets replicated at all nodes.
Replicated markers inherit the color of the nodes IF the NodeMarker
has no color attribute.
22 Oct 2010, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added -RenderMode option to control how a surface is rendered
This option is the same as Surface Controller-->RenderMode menu
22 Oct 2010, ZS Saad, ConvexHull, level 2 (MINOR), type 2 (NEW_OPT)
Added -q_opt option to allow for delaunay triangulation of 2D coordinates
This new option makes it easy to create a surface from a set
of ECOG electrodes.
20 Oct 2010, ZS Saad, afni-general, level 2 (MINOR), type 5 (MODIFY)
Added NI_duplicate* functions to niml
20 Oct 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -tcat_remove_last_trs, -ricor_regs_rm_nlast
Added for J Czarapata.
20 Oct 2010, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sort_by_acq_time for -dicom_org on Philips data
Added for Manjula.
19 Oct 2010, ZS Saad, 3dcopy, level 2 (MINOR), type 5 (MODIFY)
Allowed 3dcopy to take . or ./ as output options
Other changes make the error message a little more
informative
15 Oct 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -multi_timing_to_events, -multi_timing_to_event_pair, -per_run
- Modified timing_tool.py, lib_timing.py, lib_textdata.py, afni_util.py.
- Added for N Adleman.
12 Oct 2010, DR Glen, 3dDTtoDWI, level 2 (MINOR), type 1 (NEW_PROG)
Program to compute DWI images from diffusion tensor
Release from old code, bug fix for scale factors and lower
triangular order.
07 Oct 2010, DR Glen, Plugout commands, level 2 (MINOR), type 2 (NEW_OPT)
Commands to get current RAI xyz or IJK coordinates in a plugout script
06 Oct 2010, RW Cox, 3dttest++, level 2 (MINOR), type 2 (NEW_OPT)
Add -zskip option
Lets users skip the processing of voxel values that are
exactly zero -- to allow for non-overlap between subjects.
01 Oct 2010, DR Glen, afni GUI, level 2 (MINOR), type 4 (BUG_FIX)
Overlay color autorange, range settings not initialized properly
29 Sep 2010, G Chen, 1dSVAR.R, level 3 (MAJOR), type 1 (NEW_PROG)
Structural vector autoregression (SVAR)
This is an R program that incorporates both instantaneous and
lagged effects in an SVAR model for ROI-based network analysis.
See more details at https://afni.nimh.nih.gov/sscc/gangc/SVAR.html
27 Sep 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Began code changes to allow for volume rendering
Changes mostly involve SUMA_volume_render.c and were
made with Joachim Bottger's help. Of note is the additionof the Volume Obj
ect structure SUMA_VolumeObject.
27 Sep 2010, DR Glen, afni GUI, level 2 (MINOR), type 5 (MODIFY)
Datasets and atlas datasets show labels in overlay panel
Atlases distributed with afni have been updated to include labels
in the header that show a label for each value. If a dataset has
been created with the Draw Dataset plugin or a label table has been
applied with 3drefit, then the labels will be displayed next to the
corresponding value in the Overlay panel. Integral ROI colormaps are
used for any dataset with label tables assigned or with an INT_CMAP
attribute.
21 Sep 2010, RW Cox, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
Fix memory leak and paired t-test bug.
17 Sep 2010, RC Reynolds, 3dttest++, level 2 (MINOR), type 4 (BUG_FIX)
init workspace with 0
Trouble noted by M Choi
10 Sep 2010, DR Glen, afni_all, level 3 (MAJOR), type 5 (MODIFY)
Introduce code allowing multiple space sessions but limited to existing
spaces (ORIG, ACPC, TLRC) so should continue to be transparent.
Datasets are now tagged with space attribute, TLRC/MNI/MNI_ANAT,
and defines which kind of template a dataset has been aligned to.
This attribute is handled by @auto_tlrc, adwarp, 3drefit, whereami,
and the AFNI GUI using the whereami GUI. In the AFNI GUI, this
has the effect of allowing a dataset to be identified by its template
with the transformation to the TLRC or other atlas space handled
automatically. Other AFNI programs should apply the template space of
the master dataset or first dataset to the output.
cvs tag marked on code before this change as mid-atlantic
07 Sep 2010, ZS Saad, 3dRetinoPhase, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash caused by bad function prototype.
Crash only occurred on linux. Thanks to P. J. Kohler for
tests and bug report.
03 Sep 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed inappropriate read in SUMA_Draw_SO_Dset_Contours
This bug had caused a crash on one machine, but had the potential
for bad surprises in the future.
03 Sep 2010, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Script now process v1.label files from FreeSurfer
The output is two datasets per hemisphere, one for the ??.v1.prob.label
and one for the ??.v1.predict.label.
26 Aug 2010, ZS Saad, @auto_tlrc, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed bug in @auto_tlrc in usage 2 mode AND with no suffix
There was a bug in @auto_tlrc for the last 2 months:
from June 30, 2010 until August 26, 2010.
It occurs only when using auto_tlrc in:
usage 2 mode
AND
with -suffix omitted, or set to NONE.
This bug does not affect your data if you had used adwarp -apar,
or if you put your data in TLRC space via afni_proc.py,
or align_epi_anat.py.
The bug essentially results in a renaming of your follower dataset,
without the spatial transformation. So, if you were applying the
transform to epi+orig, it practically got renamed to epi+tlrc.
Despite the +tlrc in the name, epi+tlrc would still be in +orig
view and you no longer have epi+orig on disk.
Examples of affected commands would be:
@auto_tlrc -apar anat+tlrc -input epi+orig
or
@auto_tlrc -apar anat+tlrc -suffix NONE -input epi+orig
The script did produce Error messages but it failed to stop.
If you think you ran the buggy command (a clear symptom would be
missing +orig datasets AND bad alignment in TLRC of course), you
must download the latest binaries and rerun @auto_tlrc after you
have recreated the +orig files. You can also just get @auto_tlrc
at the link below.
Sorry for this, I had tested complicated option combinations on
the last release, but all tests had used the -suffix option.
()
Binaries postdating this message will contain the new script.
You can also get a corrected version of @auto_tlrc at this link:
Thanks To James Blair for finding the bug.
24 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Improved SUMA's DotXform (InstaCorr) and GroupInCorr interface
Changed interface so that shft+ctrl+right click is needed to initiate
callback. This makes it consistent with AFNI's interface.
shft+ctrl+right click and drag now a little faster.
23 Aug 2010, ZS Saad, SurfRetinoMap, level 3 (MAJOR), type 1 (NEW_PROG)
Calculates Visual Field Signs from visual field angle data
23 Aug 2010, ZS Saad, @RetinoProc, level 3 (MAJOR), type 1 (NEW_PROG)
Packages processing step for phase-based retinotopic mapping.
See @RetinoProc -help for details
23 Aug 2010, ZS Saad, 3dRetinoPhase, level 3 (MAJOR), type 1 (NEW_PROG)
Calculate visual field angle from phase-based retinotopy data.
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Fixed bug in sub-brick selection lists
Before the bug fix, once a sub-brick selection list was open
(right-click on 'I', 'T', or 'B') for one dataset, it never got
updated after switching to another dataset, rendering it quite useless.
Thanks to Adam Greenberg for reporting the error.
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
SUMA now detects retinotopy results and displays them appropriately
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Shift+Ctrl left, right rotates surface about Z axis
Useful for rotating flat surfaces
23 Aug 2010, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Allow users to specify colormaps for retinotopy results
See help section for variables:
SUMA_RetinoAngle_DsetColorMap and SUMA_VFR_DsetColorMap
in your ~/.sumarc, after running suma -update_env.
18 Aug 2010, ZS Saad, @DriveSuma, level 2 (MINOR), type 5 (MODIFY)
Improvements to @DriveSuma to make it more didactic
18 Aug 2010, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
changed Makefile.linux_openmp (and _64) building on F10 (was F12)
16 Aug 2010, RC Reynolds, lib_textdata.py, level 2 (MINOR), type 6 (ENHANCE)
new module to deal with reading/writing 1D/timing/married text files
heading towards handling married timing in afni_proc.py
06 Aug 2010, ZS Saad, 3dSetupGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fixed bug with LRpairs when time series had different lengths.
Also fixed minor bug with error message about data size
04 Aug 2010, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Add 'WamI' button to Clusterize GUI
Runs 'whereami -omask' and displays the output in a text window, to show
the user where the atlases think each cluster is located.
04 Aug 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_CS_NN, default to 123
Also, changed -niml to -both so that 1D files are output, and changed
the prefix to ClustSim (from rm.CS) so those files are not deleted.
If ClustSim is explicitly requested, require blur estimation.
02 Aug 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
check that stim_file/_time files match datasets, and that dsets exist
- default is to check that files are appropriate for the input data
- default is to check that input datasets exist
- added options -test_stim_files and -test_for_dsets
- afni_proc.py now depends on lib_afni1D
30 Jul 2010, RW Cox, 3dttest++, level 2 (MINOR), type 0 (GENERAL)
Renamed from 3dttest_new
Because the others in the group were whining, not wining.
Also added '-center' option to allow user a little more control over the
de-meaning of the covariates.
30 Jul 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to evaluate whether a file is valid as 1D or stim_times
Added -looks_like_1D, -looks_like_local_times, -looks_like_global_times
and -looks_like_test_all.
The main purpose is to have tests that afni_proc.py can apply.
29 Jul 2010, RW Cox, 3dttest_new, level 3 (MAJOR), type 1 (NEW_PROG)
New and improved version of 3dttest!
With covariates, including per-voxel covariates! It slices, it dices!
But wait, there's more! For no extra charge, it masks!
28 Jul 2010, ZS Saad, plugout_drive, level 2 (MINOR), type 2 (NEW_OPT)
Added SET_INDEX to plugout_drive
27 Jul 2010, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
propagate storage_mode in THD_open_tcat
This is for non-AFNI formatted datasets, and fixes the problem where
3dDeconvolve would not propagate nnodes/node_list of surface datasets.
Problem noted by N Oosterhof.
26 Jul 2010, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
Mean calculations were off for large clusters with large values.
23 Jul 2010, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add TENTzero and CSPLINzero response models
To allow the HRF to be required to be zero at the start and stop times
(i.e., it will be continuous, not suddenly drop off to zero).
23 Jul 2010, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
added Makefile.linux_openmp (and _64) for building with OpenMP support
Those distribution binaries will be built on a 64-bit Fedora 12 system.
22 Jul 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options -regress_run_clustsim and -regress_opts_CS
This is to apply 3dClustSim results for multiple comparison correction
to the stats dataset output from 3dDeconvolve.
19 Jul 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -check_afni_version and -requires_afni_version
This will allow the processing script to verify that the AFNI version
is recent enough for the enclosed commands.
19 Jul 2010, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -check_date, to verify whether the distribution is current
16 Jul 2010, RC Reynolds, 3dMean, level 2 (MINOR), type 2 (NEW_OPT)
added -mask_union and -mask_inter, for creation of mask datasets
14 Jul 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
added -mask_test_overlap and -regress_cormat_warnigns
Unless the user sets these options to 'no', the processing script
will now use 3dABoverlap to evaluate the anat/EPI mask overlap, and
1d_tool.py to check the X-matrix for large pairwise correlations
between any two regressors.
14 Jul 2010, DR Glen, afni_all, level 3 (MAJOR), type 5 (MODIFY)
Beginning to introduce code for allowing multiple spaces and atlases
These code changes should initially have no effect on functionality
and provide only a framework for introducing changes
cvs tag marked on code before this change as pre-atlantic
13 Jul 2010, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
added channel list selection, for choosing which channels to merge
13 Jul 2010, DR Glen, 3dresample, level 2 (MINOR), type 5 (MODIFY)
Allowed for wider range of voxel sizes
12 Jul 2010, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Clusterize features modified and enhanced
1) Only NN clustering is now allowed in the AFNI Clusterize GUI, and so
the only parameter left is the 'Voxels' count for the smallest cluster
to retain.
2) If attribute AFNI_CLUSTSIM_NN1 is attached (via 3dClustSim), then the
Clusterize GUI will use this to show the approximate alpha level for
each cluster -- provided the threshold has a p-value associated with it,
et cetera, et cetera, et cetera.
12 Jul 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -truncate_times and -round_times for S Durgerian
11 Jul 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE)
show TR offset stats if -tr and -show_isi_stats
08 Jul 2010, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed striping with contour objects
08 Jul 2010, G Chen, 3dICC_REML.R, level 2 (MINOR), type 1 (NEW_PROG)
IntraClass Correlation (ICC) with REML Method
This is an R program that calculates ICC with REML method on 3D
volume data based on linear mixed-effects modeling scheme. See
more details at https://afni.nimh.nih.gov/sscc/gangc/ICC_REML.html
07 Jul 2010, RW Cox, 3dClustSim, level 3 (MAJOR), type 1 (NEW_PROG)
Like AlphaSim, but faster and terser output
Computes C(p,a) = cluster size threshold for a range of p and a values:
p = per-voxel (uncorrected) threshold p-value
a = corrected probability level desired = probability of at least one
noise-only cluster happening when the cluster size threshold is C(p,a)
Optimized to use OpenMP for speed.
07 Jul 2010, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixes for large files (noted/investigated by M Hanke and Y Halchenko)
- fixed znzread/write, noting example by M Adler
- changed nifti_swap_* routines/calls to take size_t
06 Jul 2010, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added SUMA_Cmaps_Dir to point to directory with colormaps
With this environment variable, users can point to a
directory containing SUMA colormaps (*.cmap) that should
be made available to SUMA. For help on colormap file formats,
open a surface controller ('View'-->'Surface Controller'),
click on BHelp (bottom left) and then click on 'New' button
which is to the right of the colormap selector.
01 Jul 2010, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
Added -mapfile option, allowing SurfToSurf to reuse an existing mapping.
30 Jun 2010, ZS Saad, @auto_tlrc, level 2 (MINOR), type 5 (MODIFY)
Added -onewarp, and -init_xform to @auto_tlrc
I have made some small improvements to @auto_tlrc, but avoided changing
its default operation, except in one case.
In 'Usage 2', the old version performed two resampling operations. One in
3dWarp with the default quintic kernel, the other in 3dresample with the
Bk kernel. The new version can perform only one resampling thereby
reducing the smoothness of the final result. To change from the default
behavior,use the new option -onewarp.
The help output of the old version stated that -rmode controlled the
interpolation kernel in 'Usage 1'. That was not the case. In Usage 1,
interpolation was always linear. It remains so in the current version,
but the -rmode option can now be used to change the kernel.
The change in default operation between this version and the previous
concerns 'Usage 1'. In the old version, the brain was skull stripped, AND
its intensities adjusted by 3dSkullStrip. It was this adjusted brain that
was then output in TLRC space. In other terms, the output was with
no skull, but its values differed from those of the input.
This is no longer the case. In the current version, you will
get a skull-stripped version of the input in TLRC space
(no intensity adjustment).
Behavior of the -warp_orig_vol is unchanged.
This change in 'Usage 1' does not affect the registration transform,
nor 'Usage 2'.
If you insist on the old mode of operation, then contact me and I will
send you an older version of @auto_tlrc.
28 Jun 2010, RW Cox, 3dTcorr1D, level 2 (MINOR), type 0 (GENERAL)
1 output brick per column of input 1D file
Before: only used 1st column of 1D file.
Now: also uses OpenMP to parallelize across columns.
Also: -short and -mask options.
28 Jun 2010, RC Reynolds, 3dAutoTcorrelate, level 2 (MINOR), type 2 (NEW_OPT)
added -eta2 (Cohen eta squared) for HJ Jo
Also added -mask and -mask_only_targets.
22 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
3dToutcount detrending now defaults to Legendre polynomials
Using Legendre polynomials, 3dToutcount polort can exceed 3
(limit noted by I Mukai and K Bahadur).
Added options -outlier_legendre and -outlier_polort.
22 Jun 2010, RC Reynolds, 3dToutcount, level 2 (MINOR), type 2 (NEW_OPT)
added -legendre option, which also allows polort > 3
14 Jun 2010, RW Cox, AFNI GUI, level 2 (MINOR), type 5 (MODIFY)
Added 'Automask' toggle button to image viewer bar popup menu
In combination with 'Zero Color', provides an easy way to fill
the background with a solid color, such as white, as requested
by Adriana di Martino (among others).
ALSO: modified 'Zero Color' to fill zero values with that color,
rather than fill pixels assigned the bottom-most color
(so images with negative values can be treated properly).
N.B.: Automasking in the image viewer is done with a special 2D
function in thd_automask.c, different than 3D Automasking.
08 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_outliers and -regress_skip_first_outliers
08 Jun 2010, DR Glen, RetroTS.m, level 2 (MINOR), type 2 (NEW_OPT)
Allowed for alt+z2 slice timing
04 Jun 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
moved outlier counting outside of tshift block
- if only one regressor, use 1dcat for 'sum' ideal
- added -count_outliers, default to 'yes'
- outlier counting is now at end of tcat block
03 Jun 2010, RC Reynolds, plug_realtime, level 3 (MAJOR), type 6 (ENHANCE)
added ability to register merged data and possibly all channels
Via MergeRegister, one can request to register the ChannelMerge dataset.
The individual channels can also be 'registered' via the same parameters
as the ChannelMerge dataset.
Requested by J Hyde, A Jesmanowicz, D Ward of MCW.
01 Jun 2010, RC Reynolds, afni_util.py, level 2 (MINOR), type 6 (ENHANCE)
added variance and t-test routines (1-sample, paired, pooled, unpooled)
27 May 2010, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fix bug in paired t-test for covariates regression
27 May 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed use of -volreg_regress_per_run and -regress_censor_motion pair
Problem found by D Drake.
26 May 2010, RW Cox, 3dGroupInCorr, level 3 (MAJOR), type 5 (MODIFY)
Add -covariates option
With coordinated changes to AFNI to deal with the possibly more
complicated dataset that will arrive. And some minor changes to
3dSetupGroupInCorr to match.
25 May 2010, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added click and drag for third mouse button
21 May 2010, ZS Saad, SurfToSurf, level 2 (MINOR), type 2 (NEW_OPT)
Added -dset option to take in niml dsets
19 May 2010, RC Reynolds, Makefile.*, level 2 (MINOR), type 4 (BUG_FIX)
add CCOLD to all for compiling nifticdf.o on linux_xorg7_64 using gcc v3
This is a bug in the gcc compiler code, not in AFNI. So the workaround
is to compile nifticdf.o with a different version of the compiler.
The gcc compiler versions 4.1-4.3 (at least) had an optimization bug
when compiling nifticdf.o. The result was an inaccurate conversion
from F-stats to p-values (in some cases).
Test with the command: cdf -t2p fift 1.0 10 100
good result: 0.448817, bad result: 0.0472392
Problem found by L Thomas and B Bones.
18 May 2010, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
New option -vthr, to set threshold for ignoring regression vectors
In the olden version, vectors whose L1 norm was less than 0.000333 times
the largest vector's L1 norm were cast out before the analysis -- this
was to fix a problem of Rasmus Birn's. However, some people whose
initials are HJJ want to use LHS vectors whose magnitude varies a lot.
So now the user has to specify the 'cast out' vector threshold with the
-vthr option, whose default is NOT 0.000333 but is 0.0 -- that is, only
exactly zero vectors will be unused by default.
18 May 2010, DR Glen, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
Allowed for flip angle variation through volume with scaling dataset
17 May 2010, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Program would crash when only -Obuck given, no -Rstuff
Problem was that GLT data structure setup was done in the Rstuff loop,
and if no Rstuff datasets are computed, then doing GLT stuff in the
Ostuff loop would crash. Fix: test if GLTs are added to the REML setup
structures in the Ostuff loop, and add them if they aren't already
there.
12 May 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_first_trs for A Barbey
This is needed when also using -regress_censor_motion.
12 May 2010, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_first_trs, to mix with -censor_motion results
11 May 2010, DR Glen, model_demri_3, level 2 (MINOR), type 5 (MODIFY)
Changed minor defaults and error handling in DEMRI model
06 May 2010, RC Reynolds, Dimon, level 2 (MINOR), type 6 (ENHANCE)
allow negatives in -sort_by_num_suffix, look for '0054 1330' in sorting
04 May 2010, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -nzsigma to 3dROIstats
01 May 2010, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -max_consec for Liat of Cornell
30 Apr 2010, RW Cox, 3dTcorr1D, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dTcorrelate, but between a 1D file and a 3D+time dataset
Really a very simple program, with 4 options for the 'correlation'
coefficient computation: Pearson, Spearman, Quadrant, and Kendall tau_b.
28 Apr 2010, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Hide markers stuff from the user
Unless AFNI_ENABLE_MARKERS is set to YES
26 Apr 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_opts_reml
26 Apr 2010, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 6 (ENHANCE)
add $* to end of 3dREMLfit script command, for additional arguments
Finally getting around to afni_proc.py option -regress_opts_reml...
21 Apr 2010, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
-nodtrnd option was setting polort to 1, as opposed to 0.
16 Apr 2010, ZS Saad, 3dbucket, level 2 (MINOR), type 2 (NEW_OPT)
-agluto option = amalgamated -prefix and -glueto
12 Apr 2010, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Added AFNI_GUI_WRITE_AS_DECONFLICT to modify interactive 'Write' overwrite.
The default is to have the interactive 'Write' buttons overwrite existing
volumes. If this env variable is set to YES, the 'Write' behaviour follows
env AFNI_DECONFLICT
12 Apr 2010, ZS Saad, afni, level 2 (MINOR), type 4 (BUG_FIX)
Made InstaCorr SeedJump work with GroupInCorr
08 Apr 2010, RW Cox, 3dBandpass, level 2 (MINOR), type 4 (BUG_FIX)
Fix -localPV implementation
25 Mar 2010, RW Cox, help_format, level 2 (MINOR), type 5 (MODIFY)
Hyperlink refs to other program names in -help Web pages
24 Mar 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Some flexibility with animal alignment and giant move.
feature_size, rat_align options used for fineblur option
23 Mar 2010, ZS Saad, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Added -jpgs, and -pngs to allow easier size setup.
23 Mar 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_compute_fitts option, to save memory in 3dDeconvolve
19 Mar 2010, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
Added option to calculate Euclidean distance
18 Mar 2010, ZS Saad, RetroTS, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash in function remove_PNduplicates
18 Mar 2010, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Added Shft+Ctrl+click/drag to dynamic Group InstaCorr as well
18 Mar 2010, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
handle args with '\n' in them (probably from quoted newlines)
17 Mar 2010, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Add Shift+Ctrl+Button1 seed dragging in individual InstaCorr
17 Mar 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed timing_to_1D when some runs are empty
Problem found by L Thomas and B Bones.
16 Mar 2010, ZS Saad, 3dcalc, level 2 (MINOR), type 2 (NEW_OPT)
-within option to test Min <= X <= Max
16 Mar 2010, RW Cox, 3dREMLfit, level 2 (MINOR), type 5 (MODIFY)
Allow all zero columns in regression matrix, with -GOFORIT option
* Use SVD to desingularize matrix when QR factorizing (not elsewhere)
* Remove coefficients for all zero columns from GLT matrices
* Adjust DOF to compensate
* This is Thalia Wheatley's fault -- blame her for any problems
16 Mar 2010, RC Reynolds, 3dbucket, level 2 (MINOR), type 4 (BUG_FIX)
fixed getting incorrect FDR curves (noted by D Glen)
09 Mar 2010, ZS Saad, 3dclust, level 2 (MINOR), type 4 (BUG_FIX)
-isomerge and -isovalue options were being ignored
09 Mar 2010, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
-nomeanout to get rid of mean in output
08 Mar 2010, ZS Saad, 3dTcat, level 2 (MINOR), type 4 (BUG_FIX)
Program was not working with string label sub-brick selection
08 Mar 2010, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
GIfTI LabelTable format change: Index to Key
modified gifti_xml.[ch], gifti_io.[ch]
05 Mar 2010, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Added -stat P2skew to calculate Pearson's second skewness coefficient
04 Mar 2010, RW Cox, 3dGroupInCorr, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash with paired t-test opcode
Didn't switch to 1-sample mode when opcode was for paired, but no second
data vector was passed in. This, of course, is Mike Beauchamp's fault.
04 Mar 2010, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
minor changes (also see NITRC IDs 4619 and 4644)
- for integers, make default approx test to be equality
- small changes to zlib failure strings
- cast to avoid compile warning on some systems
- made NITRC gifti.dtd link that will not change
03 Mar 2010, ZS Saad, 3dmerge, level 2 (MINOR), type 2 (NEW_OPT)
-isomerge and -isovalue options that mimic 3dclust's options
03 Mar 2010, ZS Saad, 3dmerge, level 2 (MINOR), type 2 (NEW_OPT)
-1clust_depth option to determine how deep voxel is in cluster
03 Mar 2010, ZS Saad, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
-depth option to determine how deep voxel is in mask
01 Mar 2010, ZS Saad, FSread_annot, level 2 (MINOR), type 5 (MODIFY)
Allow FSread_annot to work with 2009 parcellation results.
01 Mar 2010, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Added -FSversoin, -hemi, and -FScmap* options for 2009 parcellations
01 Mar 2010, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 5 (MODIFY)
Script now deals with 2009, and 2005 parcellations.
01 Mar 2010, ZS Saad, @FS_roi_label, level 2 (MINOR), type 2 (NEW_OPT)
Modified -name to accept 'ALL'
01 Mar 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Changed default options used with giant_move and 3dAllineate.
Changed with version 1.30 of align_epi_anat.py
26 Feb 2010, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Insert Dtable structure (Label_Dtable) in dset
Inserted Dtable structure (dset->Label_Dtable) in THD_3dim_dataset.
The hash table is used to report on the label corresponding to a voxel's
integer value. Inserting a label table into the header can be done
with 3drefit.
Labels are reported in the ULay and OLay value fields in the bottom right
corner of AFNI's Define Overlay panel. The hint at that location also
shows the labels, which could be quite long.
26 Feb 2010, ZS Saad, 3drefit, level 2 (MINOR), type 2 (NEW_OPT)
-labeltable option to add a label table to a dataset
24 Feb 2010, RW Cox, 3dAllineate, level 2 (MINOR), type 2 (NEW_OPT)
New cost functional -lpc+
Combination of lpc + hel + crA + nmi + mi.
Also some micro changes to allow more -twobest starting points and the
like.
20 Feb 2010, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -timing_to_1D, -tr and -min_frac for PPI scripting (and B Benson)
15 Feb 2010, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Automatically setup range and sign for ROI colorbars
15 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
-arg*1 options to keep from getting 0 in arg* output
15 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
-*mask options to allow masking
12 Feb 2010, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Better setup of left and right flat surfaces.
12 Feb 2010, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
-*_cut_surfaces to deal with bad triangles on standard flat surfaces
12 Feb 2010, ZS Saad, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
Added -argmin1, -argmax1, -argabsmax1 options to increment argument by 1
09 Feb 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Fixed silly bug introduced in previous version
isdigit() method not called properly (Thanks Rick)
05 Feb 2010, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
thd_gifti: if LabelTable use INTENT_LABEL, suma_gifti.c: no normals
done with Ziad
03 Feb 2010, RW Cox, Group InstaCorr, level 2 (MINOR), type 0 (GENERAL)
2-sample case now also sends back 1-sample results
With this, you can look at the 2-sample difference in controller A, and
the 2 1-sample results in controllers B and C. This lets you see the
difference AND similarities at the same time.
28 Jan 2010, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
Options for multiple cost functionals,edge control
multi_cost option for trying out different cost functionals.
check_cost option for comparing for big differences among cost
functionals
edge_erodelevel option for adjusting the number of layers to erode
for edge option
14 Jan 2010, ZS Saad, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Added -rank and -frank options to 3dLocalstat
14 Jan 2010, RC Reynolds, 3dVol2Surf, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash w/labels on '-map_func seg_vals' -> NIML
Problem found by Swaroop at Dartmouth.
06 Jan 2010, RC Reynolds, thd_intlist.c, level 2 (MINOR), type 4 (BUG_FIX)
fixed sub-brick selection of datasets without labels (e.g. NIfTI)
31 Dec 2009, RW Cox, 3dGroupInCorr, level 3 (MAJOR), type 1 (NEW_PROG)
Group InstaCorr
With changes to afni and also new program 3dSetupGroupInCorr
24 Dec 2009, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -approx_gifti option
24 Dec 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
added approximate difference functions
- added gifti_approx_gifti_images, DA_pair, labeltables, diff_offset
- added gifti_triangle_diff_offset
- gifti_compare_coordsys takes comp_data param
15 Dec 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Allow label based sub-brick selection in AFNI and SUMA
15 Dec 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 4 (BUG_FIX)
Fixed 2 problems with -ort option
1) It didn't work, since the wrong array name was used :-(
2) It could fail, since the detrend routine didn't like collinear orts
-- replaced it with one that is happier with such things.
14 Dec 2009, DR Glen, McRetroTS, level 2 (MINOR), type 4 (BUG_FIX)
Variable Opt parameters were not parsed correctly
Options structure fields should be added correctly into Opt structure
12 Dec 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
modify parsimonious fit index to be based on null model
Previous calculation used chi-square from minimum model without adjusting
for number of parameters in model.
08 Dec 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
added ability to read/write GIFTI LabelTables with colors in thd_gifti.c
03 Dec 2009, RW Cox, 3dLocalPV, level 2 (MINOR), type 1 (NEW_PROG)
Speeded up version of 3dLocalSVD
Speed comes with some small limitations. About 30% faster.
01 Dec 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
Ignore triangles from Caret with nodes that have all zero coords
Not doing so results in bad display of some flat meshes because
the .topo file contains triangles with nodes that appear masked by
0.0 0.0 0.0 in the .coord file
01 Dec 2009, ZS Saad, @SUMA_Make_Spec_Caret, level 2 (MINOR), type 4 (BUG_FIX)
Improved script to make it pick up new naming convention.
30 Nov 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
afni crashes on short ANALYZE file from double fclose()
25 Nov 2009, ZS Saad, MapIcosahedron, level 3 (MAJOR), type 2 (NEW_OPT)
Added -NN_dset_map and -dset_map options to map dsets onto new meshes
The program now automatically warps LabelDsets specified in the spec
file, or any dataset specified on the command line.
24 Nov 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 4 (BUG_FIX)
Stopped writing empty attributes which caused trouble in AFNI.
Empty attributes make AFNI halt the parsing of the header.
24 Nov 2009, ZS Saad, 1dmatcalc, level 2 (MINOR), type 2 (NEW_OPT)
Added &read4x4Xform to read in spatial affine transformations.
1dmatcalc can now take in spatial affine transforms in vector
or matrix form
23 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Workaround for connection drop between AFNI and SUMA in Shared Memory Mode.
Env SUMA_AttemptTalkRecover allows SUMA to recover from drop.
This ENV is set by default to No.
23 Nov 2009, G Chen, 3dKS.R, level 2 (MINOR), type 1 (NEW_PROG)
Kolmogorov-Smirnov test
This is an R program that runs Kolmogrov-Smirnov test between
two groups of subjects. It takes individual sub-brick files from
each subject as input and spills two sub-bricks in the output,
first one being the Kolmogorov-Smirnov statistic D, while the 2nd
the corresponding Z-score.
20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
apply_prefix option to save automasked input
avoids 3dcalc step that is usually used to apply an automask.
19 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed recorder lag on OS X machines.
On OS X platforms, the 'r' or 'R' recording modes
used to record the previous image it seems.
17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
SUMA now handles labeled datatets in a special manner
An example of a labeled dataset would be FreeSurfer's annotation files.
If an annotation file is present in the spec file (@SUMA_Make_Spec_FS),
SUMA will display it as part of the background.
You can chose to display the labeled dataset in color, contours, or both.
Data from labeled datasets is now shown under the 'Lbl' field in the
surface controller's Xhair block.
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_AlwaysAssignSurface (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_LabelDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ConvexityDsetOpacity (see suma -environment for details)
17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
SUMA_ShowLabelDsetAtStartup (see suma -environment for details)
17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
Option -label_dset creates a labeled dataset from ROIs.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Option -dset creates a labeled dataset from annotation file.
Labeled datasets are now rendered in a special manner in SUMA
17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
Script now automatically sets up the spec file with labeled datasets
Labeled datasets are created from annotation files,
and are now rendered in a special manner in SUMA
16 Nov 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
allow motion censoring with varying run lengths
Also, if a max is applied in scaling, explicitly limit to [0,max].
16 Nov 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
allow motion censoring with varying run lengths
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to check for, and correct 'bowties' in pathches.
Bowties in patches result in non 2-manifold stiched surfaces whose
volume cannot be calculated. The *bowtie option deal with such cases.
09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
Added options to shrink patch contours at nodes not in selected nodes.
See options -adjust_contour for details.
09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
Added option for improved node volume estimation.
The new measure, called node_volg, uses Gauss' Theorem to estimate
the volume associated with a node in two isotopic surfaces. This option
is more robust to surface curvature variations.
04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
3dAllineate option for motion correction
volreg_method allows 3dAllineate, which is useful for DTI data.
Bug fix for post-transformation matrix and dataset view
27 Oct 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 6 (ENHANCE)
added support for optional LabelTable RGBA attributes
23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -censor_fill and -censor_fill_par
These options are to zero-pad TRs that were censored by 3dDeconvolve.
19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for using 3dBlurInMask, instead of 3dmerge
- added -blur_in_mask, -blur_in_automask and -blur_opts_BIM
- added -sep_char and -subj_curly
19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT)
New master options, dset1/2 terminology
New master_nnn_dxyz options to specify output resolution
dset1 and dset2 for non-EPI/anat alignment with lpa cost function
and turns off preprocessing steps
giant_move option turns off resampling and changes master options
Expanded help - including fuller description of edge method
Removed volume registration (motion correction) for anat2epi option
by default.
AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output
depending on BASE, SOURCE or external dataset names for all output
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Direct viewing of pre-processed datasets in Dot xform
14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
New help window for Dot xform
07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
Add -Mmask option to allow multiple mask values
For independent blurring (e.g., blur WM and GM separately).
06 Oct 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
More bug fixes related to ROI loading, and OSX's GLX problem
29 Sep 2009, RW Cox, afni, level 3 (MAJOR), type 5 (MODIFY)
InstaCalc is more-or-less ready
At least, I let Mike Beauchamp test it for his cunning plans.
29 Sep 2009, RC Reynolds, @Reorder, level 2 (MINOR), type 1 (NEW_PROG)
script version of reorder plugin, for J. Bjork
29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Flexible slice timing options
SliceOrder option allows for standard slice timing order
alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input
29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT)
Opt options available to compiled version
All options available through the Opt structure are now available
even with the compiled version of McRetroTS, making the compiled version
functionally equivalent to the RetroTS.m version
24 Sep 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed crashes on OS X 10.5 caused by OS X's buggy GLX implementation
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Improved the 'star' blurring interface.
24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Setup final color blurring level.
18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Added option -n minnodes
18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying external FreeSurfer color table.
16 Sep 2009, RC Reynolds, 3ddot, level 2 (MINOR), type 4 (BUG_FIX)
de-meaning data causes permission-based seg fault, apply means upon read
Problem found by Giuseppe Pagnoni.
14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
Allow specifying rmm in number of edges connecting nodes.
09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT)
Allow @fast_roi to accept existing TLRC transformed anatomy
09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
Add 'ball' options for mask generation
08 Sep 2009, DR Glen, whereami, level 2 (MINOR), type 5 (MODIFY)
Allows MNI_ANAT space for whereami
Subtracts 8mm I-S and uses MNI space transform to TTA
08 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Properly allows post-transformation matrix
04 Sep 2009, RC Reynolds, plug_realtime, level 2 (MINOR), type 6 (ENHANCE)
registration can now be consistent across runs
Reg Base can be 'Current': to set the base volume from the current run
(call this the old way), 'Current & Keep': use current run, but then
store that base and apply it to future runs, 'External Dataset': fix the
base from some chosen dataset.
Using 'Current & Keep' makes sense for realtime registration.
03 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes for certain combinations
Allowed BASE and SOURCE specification for oblique data
Allowed 3dWarpDrive volume registration with mean/max base
Removed anatomical output with oblique data and only epi2anat
26 Aug 2009, RW Cox, 3dFFT, level 2 (MINOR), type 1 (NEW_PROG)
Compute spatial 3D FFT of a dataset
* This is for John Butman
* Was started a long time ago, but only finished today
* Probably useless
25 Aug 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Provide keystroke fine control over cropping in image viewer
Shift+arrowkey = scroll crop window
Ctrl+arrowkey = resize crop window
Right-click on crop button = menu to set size exactly
Hint on crop button = shows crop parameters
25 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
if volreg block, always create motion_${subj}_enorm.1D
21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_censor_motion and -regress_censor_prev
Motivated by L Thomas and B Bones.
20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added motion censoring options
Added -censor_motion, -censor_prev_TR, -collapse_cols, -extreme_mask,
-set_tr, -write_censor and -write_CENSORTR.
Also modified afni_util.py, lib_afni1D.py and option_list.py.
14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -align_epi_ext_dset, to align anat to external EPI
This may be important for multi-channel coil EPI data with low internal
structural contrast. Users might align to the first (pre-steady-state)
TR, even though that volume is not used in the analysis.
13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_tlrc_adwarp, to apply a manual Talairach transformation
10 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
truncate min dim to 3 sig bits for -volreg_tlrc_warp/-volreg_align_e2s
The old default was 2 bits, -volreg_warp_dxyz overrides.
10 Aug 2009, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 6 (ENHANCE)
allow processing of -overwrite and AFNI_DECONFLICT
06 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed problems found by I Mukai and K Bahadur
- fixed -volreg_align_to base as applied in align_epi_anat.py
- fixed blur 'averages' computation when only one run
04 Aug 2009, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 6 (ENHANCE)
added basic demo interface and itemized exception traps
29 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed creation of extents mask when only 1 run
28 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 5 (MODIFY)
if known, require proper slice regressor ordering in -slibase* opts
27 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
use -slibase_sm instead of -slibase in 3dREMLfit
27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -slibase_sm, for slice-major ordering of regressors
RetroTS and afni_proc.py were incorrectly using this ordering.
** Analysis done prior to this probably needs to be re-done.
27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_labels and -show_label_ordering
23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -partition option
23 Jul 2009, RC Reynolds, afni_run_R, level 2 (MINOR), type 6 (ENHANCE)
allow any number of args, but where first is program, last is output
23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT)
Single and Dual exponential models
New models for 3dNLfim that use single and dual exponential models
that are appropriate for MEMRI (Manganese Enhanced MRI
22 Jul 2009, RC Reynolds, realtime_receiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
python replacement for serial helper
New 'data_choice' options can be added to compute_data_for_serial_port
for sending results of a different computation to the serial port.
21 Jul 2009, RW Cox, niml_feedme, level 2 (MINOR), type 1 (NEW_PROG)
Test and demo program showing how to set datasets to AFNI via NIML
An analog to rtfeedme. Sends volumes to AFNI using VOLUME_DATA
elements. Pretty rudimentary.
21 Jul 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Update widgets and viewing when VOLUME_DATA is added to a dataset
* Fix AFNI_setup_viewing() to update widgets properly when dataset nvals
changes
* Add function AFNI_update_dataset_viewing() to deal with viewing
changes that might be needed if a dataset is altered
16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
Added option to force autoscale on the graphing window
The option is accessible by pressing 'A' in the graph window
or under 'Graph->Opt->Scale->AUTO'.
14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -max_rest, to limit the maximum duration of rest periods
14 Jul 2009, DR Glen, afni, level 2 (MINOR), type 3 (NEW_ENV)
Added AFNI_ONE_OBLIQUE_WARNING
AFNI_ONE_OBLIQUE_WARNING = YES makes interactive spit out ONE warning
about obliquity per session then go quiet.
13 Jul 2009, RW Cox, 3dLocalstat, level 2 (MINOR), type 5 (MODIFY)
OpenMP
Also added option '-use_nonmask' to allow statistics to be computed for
voxels not in the mask (but presumably whose neighbors are in the mask).
25 Jun 2009, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
fixed dz sent to RT plugin for oblique datasets
24 Jun 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 0 (GENERAL)
Modify to use OpenMP more effectively.
Have to avoid use of Doug's matrix.c functions in the main loops, since
they do so much malloc/free, which blocks other threads from running.
Instead, rewrote versions of the needed functions that use pre-allocated
workspace arrays. Speedup is very good now for the REML setup and REML
voxel loops. Haven't decided whether to OpenMP-ize the GLSQ or OLSQ
loops, since these usually take much less time.
24 Jun 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
applied print changes from B Feige (26 files):
3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c
suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c
SUMA/ SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c
SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c
SUMA_ParseCommands.h SUMA_SphericalMapping.c
SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c
SUMA_compare_surfaces.c SUMA_xColBar.c
svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c
23 Jun 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
added 4 checks of alloc() returns
17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
version 2.0 : call e2a alignment and warp to standard space ready
- mask warped EPI by its extents (at volreg step)
- added -volreg_no_extent_mask, to block this masking
- added 'extents' to list of mask in -mask_apply
- change block dividers to more visual '===' with block names
17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -make_3dd_contrasts and used general accuracy in block durations
17 Jun 2009, DR Glen, RetroTS.m, level 2 (MINOR), type 4 (BUG_FIX)
Number of TRs found incorrectly because of rounding
17 Jun 2009, DR Glen, McRetroTS.m, level 2 (MINOR), type 1 (NEW_PROG)
Matlab Compilable version of RetroTS.m
This version calls the RetroTS function, but can be compiled
for users that either do not have Matlab, a required toolbox
or want to use this function in a shell script more easily.
15 Jun 2009, RC Reynolds, 3dmerge, level 2 (MINOR), type 6 (ENHANCE)
allowed short/byte datasets to use FIR blur, so no Fourier interpolation
Also added Y/N AFNI_BLUR_INTS_AS_OLD env var to use previous method.
15 Jun 2009, DR Glen, BrikLoad.m, level 2 (MINOR), type 4 (BUG_FIX)
Typo in BrikLoad
Gremlin got to Pixy
11 Jun 2009, RW Cox, AlphaSim, level 2 (MINOR), type 5 (MODIFY)
Added computation of analytic approximation of Alpha(i) for large i
Uses a modified extreme value distribution, which looks pretty good.
11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added masking abilities
- in mask block, try to create anat and group masks
- added -mask_apply option, for choosing mask to apply to regression
- added -align_opts_aea, for extra opts to align_epi_anat.py
29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -execute and now fail if block options have no corresponding blocks
28 May 2009, RC Reynolds, strblast, level 2 (MINOR), type 4 (BUG_FIX)
partial words had resulted in skipping ahead
found by R Notestine of UCSD
28 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 0 (GENERAL)
example updates for AFNI_data4 and new options
27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
updates for alignment/warp/varying run lengths
- added -volreg_warp_dxyz option
- if align a2e, add -no_ss to @auto_tlrc
- for varying run lengths, fixed application of '-volreg_align_to last'
and the -regress_est_blur_* options
(blur estimation loops were modified for this)
- warping to new grid truncates to 2 significant bits (if < 2 mm)
22 May 2009, ZS Saad, @FS_roi_label, level 2 (MINOR), type 1 (NEW_PROG)
A script to get FreeSurfer parcellation and annotation labels
The script is used to return a label associated with a FreeSurfer
annotation or parcellation integer label.
21 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Additional check for caret-version string
It seems that the syntax for caret-version has changed
slightly and was being missed by SUMA. As a result, Caret
surfaces were not being properly aligned with the volumes.
21 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added 'align' processing block and -volreg_align_e2a option
20 May 2009, RW Cox, realtime plugin, level 2 (MINOR), type 5 (MODIFY)
Modified to allow realtime 3D registration on complex inputs
Mostly a change in mri_3dalign.c, to take the movement estimation done
on the magnitude image and apply it to the 2 component images.
20 May 2009, G Chen, 3dMEMA.R, level 4 (SUPER), type 1 (NEW_PROG)
Mixed-Effects Meta Analysis (MEMA)
This is an R program that runs group analysis in a truly random
mixed-effects sense by taking both beta and t-statistic as input
instead of beta value only in the conventional method. See more
details at https://afni.nimh.nih.gov/sscc/gangc/MEMA.html
19 May 2009, ZS Saad, @ROI_Corr_Mat, level 3 (MAJOR), type 1 (NEW_PROG)
A script to calculate correlation matrices between ROI time series
Calculates the correlation matrices between average time series from ROIs
defined in a mask volume. Script was written with Hang Joon Jo.
19 May 2009, ZS Saad, prompt_user, level 2 (MINOR), type 1 (NEW_PROG)
Prompts user for input with an X window
19 May 2009, ZS Saad, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
Added -zerofill and -roisel options
Added options to force output for empty ROIs.
19 May 2009, ZS Saad, 1ddot, level 2 (MINOR), type 2 (NEW_OPT)
Added -okzero to keep program from exiting with all zero input
Added options to force output for empty ROIs.
15 May 2009, RW Cox, afni InstaCorr, level 2 (MINOR), type 0 (GENERAL)
Remove OpenMP; carry out setref on all locked controllers
15 May 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
added -volreg_tlrc_warp option: can warp to standard space at volreg step
13 May 2009, RW Cox, InstaCorr+3dBlurInMask, level 2 (MINOR), type 0 (GENERAL)
Added OpenMP support for blurring to these programs
Parallelization occurs across sub-bricks -- speedup is significant.
11 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
InstaCorr changes
* Save seed time series into the 1D timeseries library for graphicking
* Modify progress printouts slightly
08 May 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Better display of ROI contours on patches
Suma now correctly handles ROI display when the ROIs
contain nodes that are not in the patch. Also, on flat surfaces,
ROI contours are drawn raised so that they float over flat surfaces.
08 May 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
The script now automatically turns FS annot files to SUMA ROI files
08 May 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Instacorr updates
* Can Write A_ICOR datasets using new allow_directwrite variable
* Disable InstaCorr when switching sessions and views
* Notify renderer (DRAWNOTICE) when changes made
* Shift-Ctrl-Left-Click does crosshair shift + InstaCorr Set
07 May 2009, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
FIxes/upgrades for InstaCorr
* memory problem fixed by malloc-ing sizeof(float *)
-- not sizeof(float) -- for a float ** variable!
* add dataset labels
* add statistical parameters (including FDR)
* add help
06 May 2009, RW Cox, afni, level 3 (MAJOR), type 2 (NEW_OPT)
First edition of InstaCorr!
Rough around the edges, but gnarly-ific to the level of the first
inaccessible cardinal!
05 May 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 4 (BUG_FIX)
Added 'd' and 'j' keys
05 May 2009, ZS Saad, 3dRank, level 2 (MINOR), type 1 (NEW_PROG)
A program that substitutes a voxel's value by that value's rank
05 May 2009, RC Reynolds, plug_render, level 2 (MINOR), type 5 (MODIFY)
now built from plug_null.c, so it will no longer be available
05 May 2009, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 1 (NEW_PROG)
another script to update the AFNI package
01 May 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dBlurToFWHM, but simpler.
01 May 2009, DR Glen, 1dSEM, level 2 (MINOR), type 4 (BUG_FIX)
Tree growth fix
Fixed bug in tree growth and improved output text
30 Apr 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 2 (NEW_OPT)
return a node v2s time series when afni changes xhair position
30 Apr 2009, RC Reynolds, thd_niftiread, level 2 (MINOR), type 5 (MODIFY)
be sure to warn users when nifti is converted to float (w/dglen)
30 Apr 2009, RC Reynolds, 3dcalc, level 2 (MINOR), type 5 (MODIFY)
changed atan2(y,x) to proceed if y OR x is non-zero
29 Apr 2009, ZS Saad, SurfSmooth, level 2 (MINOR), type 4 (BUG_FIX)
-detprefix_* options now do something!
29 Apr 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
-nodelist* options to output node sequence forming ROI
29 Apr 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 4 (BUG_FIX)
Fixed crash when using -it option for geometry smoothing
29 Apr 2009, ZS Saad, ConvertDset, level 2 (MINOR), type 2 (NEW_OPT)
-node_select_1D now respects node ordering
29 Apr 2009, ZS Saad, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
-VarThresh* options for obtaining counts at different thresholds
29 Apr 2009, RW Cox, afni, level 2 (MINOR), type 3 (NEW_ENV)
Make 'Where am I?' font size user controllable.
via AFNI_TTATLAS_FONTSIZE environment variable (editable).
29 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
when opening -geomparent, allow for known non-afni extensions
28 Apr 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add duration argument to SPMGx basis functions for deconvolution.
For Tracy Doty, apparently.
28 Apr 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 5 (MODIFY)
uppercase file extensions are now valid
23 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
updates to help and tcsh options
- added -f as a recommended tcsh option
- added help section 'SCRIPT EXECUTION NOTE'
- reordered help: intro, BLOCKS, DEFAULTS, EXAMPLES, NOTEs, OPTIONS
- shifted execution command to separate line
22 Apr 2009, DR Glen, @AddEdge, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique edge display
Fixed bug with oblique data in edge display
16 Apr 2009, RW Cox, All, level 2 (MINOR), type 4 (BUG_FIX)
Inadvertent recursion in afni_environ.c now blocked.
14 Apr 2009, ZS Saad, suma-general, level 2 (MINOR), type 4 (BUG_FIX)
niml ROI files with empty ROI no longer crash suma/ROI2dataset
14 Apr 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added sample nifticlib program: clib_01_read_write.c
11 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -volreg_regress_per_run
This is to apply the motion parameters of each run as separate regressors.
11 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -derivative and -set_nruns, fixed -show_cormat_warnings typo
10 Apr 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Error in processing -slibase file with censoring
Typo in replacing input image with censored image caused the end of the
world (SEGV crash).
10 Apr 2009, RC Reynolds, to3d, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
Can also use AFNI_DICOM_USE_LAST_ELEMENT environment variable.
10 Apr 2009, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -use_last_elem option for setting DICOM elements
10 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
fix for old versions of python, like on solaris
Each of copy.deepcopy(), sum(), and sort(reverse=True) failed.
09 Apr 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
'official' release with RETROICOR processing block: ricor
o added 'across-runs' ricor_regress_method
o added ricor information and usage to help (see 'RETROICOR NOTE')
o maintain unscaled shorts if they are input
o added -ricor_datum
09 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_cormat_warnings and -cormat_cutoff
08 Apr 2009, RW Cox, thd_filestuff.c, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_ALLOW_ARBITRARY_FILENAMES
Set this environment variable to YES to allow 'strange' characters into
AFNI created filenames. You should know what you are doing if you use
this variable!
08 Apr 2009, RW Cox, AFNI image viewer, level 2 (MINOR), type 5 (MODIFY)
Set MPEG 'pattern' for frames to reflect the Anim_dup setting.
This small change will make MPEG-1 (.mpg) files that are slowed down by
setting Anim_dup > 1 not significantly larger than full speed files, by
setting the frame pattern to 'IPPPP' where the number of Ps is the
number of duplicate frames (Anim_dup-1).
08 Apr 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_rows_cols option
06 Apr 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '.', ',', and space keys, and 'shw_0'
04 Apr 2009, RW Cox, 3dmaskSVD, level 2 (MINOR), type 1 (NEW_PROG)
Like 3dmaskave, but does SVD principal vector instead of average
02 Apr 2009, RW Cox, 3dTcorrMap, level 2 (MINOR), type 2 (NEW_OPT)
Add -Thresh option
To save a count of how many other voxels are above threshold correlated
with each seed voxel.
02 Apr 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
changed CHECK_NIFTI to CHECK_NEEDS_FLOATS, including other dset types
01 Apr 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Arrow keys based navigation along surface.
See 'Alt+U-D' section in SUMA's interactive usage help.
01 Apr 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
added 'ricor' processing block, for RETROICOR regressor removal
31 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Handling of double precision datatypes.
31 Mar 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added 'on the fly' dot product computation
This feature is only available with SUMA's -dev
option. It is still in testing mode and its
interface may change. If intrigued, see 'D' key's
help in SUMA's interactive usage help.
31 Mar 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added support for '[' and ']' keys and -view_surf
31 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
small changes, and prep for retroicor
- by default, the script will now terminate on any error
- added -exit_on_error, -check_setup_errors
- whine about block order problems
31 Mar 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -pad_to_many_runs, -reverse
30 Mar 2009, RW Cox, 3dABoverlap, level 2 (MINOR), type 1 (NEW_PROG)
Computes various overlap and non-overlap statistics for 2 datasets.
Will resample dataset #B to match dataset #A, if needed. This program
is intended to check if two datasets are grossly not aligned, and has
little other purpose.
27 Mar 2009, RW Cox, FDR calculations, level 2 (MINOR), type 5 (MODIFY)
Changes/additions to mask operations for FDR curves.
3dREMLfit and 3dDeconvolve now generate an automask for the FDR curving
purposes, if no other mask is used. 3drefit has a new -FDRmask option
for computing the FDR curves correctly if no mask was used before.
26 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
Support for reading/writing MNI .obj surfaces
25 Mar 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add -nobout option, to suppress baseline betas from -Rbeta/-Obeta.
Per the request of Michael S Beauchamp, University of Texas.
25 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
+view now comes from data: so it works with +tlrc
24 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
by default now, no mask is applied in the scale and regression steps
Also added -regress_apply_mask option.
20 Mar 2009, RC Reynolds, @build_afni_Xlib, level 2 (MINOR), type 1 (NEW_PROG)
moved from X/@build.Xlib, for distribution
and added to SCRIPTS for building afni_src.tgz in Makefile.INCLUDE
19 Mar 2009, RC Reynolds, 1d_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
added lib_afni1D.py and 1d_tool.py
This is a library and tool for manipulating 1D files.
Many functions will still be added.
19 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 2 (NEW_OPT)
added -verbose_opts option, for being verbose during option processing
19 Mar 2009, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
a few additions and changes
- allow container chars (e.g. []) in decode_1D_ints()
- added is_valid_int_list()
- changed str vars to istr (as str is a keyword)
18 Mar 2009, RC Reynolds, eg_main_chrono.py, level 2 (MINOR), type 1 (NEW_PROG)
sample main python program using a library and chronological options
18 Mar 2009, DR Glen, 3dZcat, 3daxialize, level 2 (MINOR), type 2 (NEW_OPT)
NIFTI support
Fixed support for NIFTI output in 3dZcat and 3daxialize
Added -frugal option to 3daxialize to keep old behavior
for AFNI format datasets. Existing -frugal option in
3dZcat imposes 'oldish' behavior too.
16 Mar 2009, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
malloc extra val in case of percentile truncation
12 Mar 2009, ZS Saad, suma-general, level 2 (MINOR), type 2 (NEW_OPT)
SUMA talks to matlab.
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
warn user about masking in orig space
- if despiking and no regression mask, apply -nomask
- added 'MASKING NOTE', to suggest no regression mask until group space
12 Mar 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_reml_exec and -regress_3dD_stop
One can execute 3dREMLfit and/or 3dDeconvolve. Error blur is from each.
11 Mar 2009, RW Cox, 3dANOVA, level 2 (MINOR), type 2 (NEW_OPT)
Add -mask option to 3dANOVA, 3dANOVA2, 3dANOVA3
10 Mar 2009, DR Glen, 3dLocalstat, level 2 (MINOR), type 2 (NEW_OPT)
Sum option
Sum option (for functional weighting of interiorosity measure)
06 Mar 2009, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Add 'WAV' function (from waver) to -stim_times repertoire.
06 Mar 2009, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
if mri_automask_image() input is not really 3D, only apply clip
3dD uses automask for misfit warning, let this apply to niml.dset
05 Mar 2009, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
free vox_warp via KILL_list rather than directly when deleting dataset
Fixes afni crash: set acpc markers -> acpc view -> orig view
-> new markers -> acpc view -> death ...
04 Mar 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added openmotif build tree, updated @build.Xlib and README under X
03 Mar 2009, RC Reynolds, @build.Xlib, level 2 (MINOR), type 1 (NEW_PROG)
this is a build script for the local X packages
02 Mar 2009, RW Cox, zfun, level 2 (MINOR), type 0 (GENERAL)
add compression functions (using zlib) to libmri in zfun.c
27 Feb 2009, RC Reynolds, X-general, level 2 (MINOR), type 5 (MODIFY)
added lesstif and libXt trees to cvs
11 Feb 2009, RW Cox, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
replace DMAT_svdrot_old with DMAT_svdrot_newer
Old function fails sometimes, making the output rotation be garbage and
producing junk image results; the newer one seems more robust.
09 Feb 2009, RW Cox, imseq.c, level 2 (MINOR), type 3 (NEW_ENV)
Add AFNI_ANIM_DUP environment variable.
Allows user to duplicate images when writing an animation (AGIF or
MPEG) file. A simple and stoopid way to slow down an MPEG.
09 Feb 2009, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
random updates, plus those for Fedora 10
04 Feb 2009, RC Reynolds, vol2surf, level 2 (MINOR), type 4 (BUG_FIX)
fixed norm reversal application and norm dir check computation
Thanks to Xiaopeng Zong for finding these problems.
02 Feb 2009, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
SurfDist now outputs distances from one node to a set of other nodes
02 Feb 2009, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
Added load_col option to DriveSuma
02 Feb 2009, RW Cox, parser (calc programs), level 2 (MINOR), type 5 (MODIFY)
Add hrfbk4 and hrfbk5(t,T) functions to parser
To imitate the BLOCK4 and BLOCK5 response functions in 3dDeconvolve.
13 Jan 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 1 (NEW_PROG)
Added GS_orth_1D.m to perform Gram-Schmidt orthogonalization
13 Jan 2009, ZS Saad, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
AFNI should now be Lesstif compliant
Made numerous changes with Rick Reynolds. The biggest modification
regards buttons inside popup menus. Those buttons are no longer
inside rowcolumn widgets and had to be directly managed by afni.
05 Jan 2009, ZS Saad, MapIcosahedron, level 2 (MINOR), type 2 (NEW_OPT)
Program no longer confined to FreeSurfer surfaces
The program now allows the user to specify any morph sphere,
not just sphere.reg or sphere. This required rewriting much of
of the program's main section but the algorithm for the mapping
remains unchanged.
31 Dec 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
fix for lesstif crash on 'where am i', along with ziad
30 Dec 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
For FALTUNG, use sparse matrix operations for pure least squares.
Deconvolution + penalty matrix is sparse. Uses the 'rcmat' functions
originally developed for 3dREMLfit. Speeds things up a lot when the
time series is long.
22 Dec 2008, G Chen, 3dICC.R, level 3 (MAJOR), type 1 (NEW_PROG)
IntraClass Correlation (ICC) with ANOVA scheme
This is an R program that calculates ICC on 3D volume data based on a
two- or three-way random-effects ANOVA scheme. See more details at
https://afni.nimh.nih.gov/sscc/gangc/ICC
16 Dec 2008, G Chen, 3dGC.R, level 3 (MAJOR), type 1 (NEW_PROG)
Bivariate Granger causality analysis
This is an R program that runs Granger causality analysis with a
seed region versus the rest of the brain. See more details at
https://afni.nimh.nih.gov/sscc/gangc/3dGC
13 Dec 2008, ZS Saad, afni-matlab, level 3 (MAJOR), type 1 (NEW_PROG)
RetroTS creates regressors for cardiac, respiratory, and RVT filtering
RetroTS.m and accompanying functions create slice-based regressors
for regressing out the effects of cardiac, respiratory, and RVT effects
from FMRI time series. The regressors generated are meant to be used
with 3dREMLfit.
11 Dec 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed -slibase bug.
Oopsie. -slibase didn't work properly with more than 1 added column per
slice. Also, per the request of ZSS, you can now input more than 1
column set per image file, in repetitive slice order:
0 1 2 3 0 1 2 3 0 1 2 3
if there are 4 slices in the dataset, for example.
10 Dec 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added new options for extra stimuli, RONI and an external volreg base
- allow NIfTI datasets as input (but process as AFNI)
- added -regress_extra_stim_files and -regress_extra_stim_labels
- added -regress_RONI and -volreg_base_dset (for Jill Weisberg)
09 Dec 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
Fixed (potential) SUMA crash when Draw ROI interface is first opened
09 Dec 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 2 (NEW_OPT)
Added -cm option to allow centering based on the center of mass
09 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
Added 'dmBLOCK' to the '-stim_times_IM' repertoire.
05 Dec 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Siemens DICOM handling
added -oblique_origin and -reverse_list to help handle Siemens
DICOM data. oblique_origin option added to to3d and 3drefit
Rick added flipped slice handling to oblique mosaic handling
04 Dec 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 2 (NEW_OPT)
Extend -stim_times_AM2 option to allow multiple amplitudes
04 Dec 2008, RW Cox, 1dMarry, level 2 (MINOR), type 5 (MODIFY)
Allow multiple marriages, to go with 3dDeconvolve changes
04 Dec 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
added balloon target for M Belmonte
Also modified Makefile.linux_xorg7_64 and macosx_10.4_G5/Intel and 5_Int*.
02 Dec 2008, ZS Saad, SpharmReco, level 3 (MAJOR), type 1 (NEW_PROG)
Reconstructs data from spherical harmonics decomposition.
See SpharmDeco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, SpharmDeco, level 3 (MAJOR), type 1 (NEW_PROG)
Performs spherical harmonics decomposition.
This program performs spherical harmonics decomposition
for surfaces' geometry and/or surface-based data
See SpharmReco -help and the demo script @Spharm.examples
for details.
02 Dec 2008, ZS Saad, @Spharm.examples, level 3 (MAJOR), type 1 (NEW_PROG)
A script to demonstrate the usage of SpharmDeco and SpharmReco
02 Dec 2008, ZS Saad, @NoisySkullStrip, level 3 (MAJOR), type 1 (NEW_PROG)
A script to improve skull stripping in noisy of heavily shaded data
01 Dec 2008, RC Reynolds, timing_tool.py, level 3 (MAJOR), type 1 (NEW_PROG)
a tool for manipulating and evaluating stimulus timing files
This is useful for getting statistics on rest timing.
24 Nov 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added options -infile_list and -show_sorted_list
The -show_sorted_list option will print a list of files by run/index.
21 Nov 2008, ZS Saad, @fast_roi, level 3 (MAJOR), type 1 (NEW_PROG)
Creates Atlas-based ROIs in original space for real-time experiments
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added Options menu, Show Cosmat and GUI help
This is the initial release version, 1.0.
21 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test_libs option
21 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
removed 'R' from basic test list, and applied verb 2 to base usage
20 Nov 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
incorporated real-time volume writing from V. Roopchansingh of MCW
18 Nov 2008, RW Cox, 3dANOVA programs, level 2 (MINOR), type 2 (NEW_OPT)
Add option to output float-valued datasets.
Set the AFNI_FLOATIZE environment variable to YES, and the output of
3dANOVA, 3dANOVA2, and 3dANOVA3 will be stored in float format instead
of in scaled short format. [Per the request of Paul Hamilton]
18 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
added -test, -show_col_types, -show_cosmat, -show_fit_ts, -cormat_cutoff
also added the main help
13 Nov 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Added a NIDO sphere as Displayable Object
See suma -help_nido for details.
13 Nov 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -al option to use 3dAllineate -lpa
07 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
more updates:
- scipy is only tested for when necessary
- compute norms locally if no scipy
- solve_against_1D, linear_combo: return error string instead of code
- added -chrono option, to make all options chronological
(so options are essentially scriptable)
07 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
tlrc view handling
fixed view name of tlrc output with tlrc_master set to SOURCE
06 Nov 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 0 (GENERAL)
Add 'scale to shorts misfit' warning messages.
Also added to 3dcalc and some other programs.
06 Nov 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
pre-release updates:
- added many initial command-line options
- added plot_xmat_as_one toggle button
- added computation of cosine matrix and cosmat_warnings
- separated GUI code into new file gui_xmat.py
06 Nov 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 2 (NEW_OPT)
added option -full_test
06 Nov 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Oblique children handling
fixed combination of oblique with child epis for epi2anat output
04 Nov 2008, RW Cox, 3dNLfim, level 2 (MINOR), type 0 (GENERAL)
Added model_expr2.c
Model that uses an arbitrary 3dcalc-like expression with 2 free
parameters (any letters but 't', which is used for the time axis).
04 Nov 2008, RW Cox, 3dBlurToFWHM, level 2 (MINOR), type 4 (BUG_FIX)
skip all zero sub-bricks in the blurmaster - for Tomski Rosski
03 Nov 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Several changes
Finished -gltsym, -Rglt, and -Oglt options = add GLTs on the 3dREMLfit
command line and output those exclusively to new files.
Modified -addbase and -slibase to do censoring if input 1D files are the
same length as the uncensored matrix.
Also fixed bugs in -ABfile. Oopsie.
31 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -show_timing_stats option
Also, made a small change affecting timing (old results will not match).
31 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
Time axis attributes
Added support in 3drefit for applying time axis attributes
30 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
AddEdge with epi2anat
fixed AddEdge option for epi2anat output
29 Oct 2008, RC Reynolds, xmat_tool.py, level 2 (MINOR), type 5 (MODIFY)
if the X-matrix has a constant regressor, do not de-mean it
In such a case, the cormat would not exactly be a correlation matrix.
29 Oct 2008, RC Reynolds, python_module_test.py, level 2 (MINOR), type 1 (NEW_PROG)
program to test python module imports (interface to module_test_lib.py)
28 Oct 2008, RC Reynolds, module_test_lib.py, level 2 (MINOR), type 1 (NEW_PROG)
library to test python module imports
One might want to apply this module at the top of any python file.
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added -offset option
27 Oct 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 4 (BUG_FIX)
actually applied -min_rest, sorry...
27 Oct 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -regress_motion_file option
24 Oct 2008, RC Reynolds, xmat_tool.py, level 4 (SUPER), type 1 (NEW_PROG)
program to inspect a .xmat.1D X-matrix, possibly against a time series
This is a Graphical tool for plotting a design matrix, reviewing
condition numbers or the correlation matrix, and fitting to a 1D
time series.
23 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added -rout option, by popular 'demand'
23 Oct 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 4 (BUG_FIX)
removed reference to cdflib, for 'make afni_src.tgz'
20 Oct 2008, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
added write_text_to_file function
20 Oct 2008, RC Reynolds, afni_driver.c, level 2 (MINOR), type 2 (NEW_OPT)
added 'GETENV' to the list of DRIVE_AFNI commands
15 Oct 2008, RW Cox, fdrval, level 2 (MINOR), type 1 (NEW_PROG)
Compute FDR value on command line, from dataset header
15 Oct 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 4 (BUG_FIX)
Fixed errts (etc) outputs: censored values not set to zero!
15 Oct 2008, DR Glen, afni plugouts, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
quiet communications
@AddEdge silences communications as plugout
14 Oct 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
If source=scaled shorts, then output will be scaled as well.
14 Oct 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor updates
AddEdge option enhanced and help updated
14 Oct 2008, DR Glen, @AddEdge, level 2 (MINOR), type 5 (MODIFY)
Help and options
More user options, improved help, removed temporary files
09 Oct 2008, G Chen, 1dGC.R, level 4 (SUPER), type 1 (NEW_PROG)
Multivariate Granger causality analysis
This is an R program that runs Granger causality analysis among a few
pre-select regions. See more details at
https://afni.nimh.nih.gov/sscc/gangc/1dGC
06 Oct 2008, DR Glen, 3drefit, level 2 (MINOR), type 5 (MODIFY)
-atrfloat and -atrint options
Allows addition and modification of dataset attributes
including modifying IJK_TO_DICOM_REAL. Not all attributes
can be modified if fairly basic to dataset.
03 Oct 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
SUMA accepts text, images, and textures as Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs). The new DOs are in a simple
NIML format. It is simplest to look at the script @DO.examples
for illustrations of the various forms of DOs that SUMA supports.
Sample NIML DOs (called NIDOs) are now provided with the distribution
They are called demo.*.niml.do.
03 Oct 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-viewer_position/_width/_height/_size to control window placement
See DriveSuma -help for details.
03 Oct 2008, ZS Saad, @DO.examples, level 2 (MINOR), type 1 (NEW_PROG)
A script that demonstrates the use of Displayable Objects
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects (DOs).
30 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -gltsym option
Makes it easy for the user to add GLTs without using 3dDeconvolve.
29 Sep 2008, RC Reynolds, 3dmatmult, level 3 (MAJOR), type 1 (NEW_PROG)
program to multiply AFNI datasets slice-by-slice as matrices
26 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-child_anat option
Convenience option to align follower anat datasets to epi
25 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
added -usetemp option
Saves REML setup matrices for various cases to tmp disk files. Is
necessary for -slibase and -Grid 5 combined, if anyone ever actually
wants to run such a case.
24 Sep 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
-addbase and -slibase options to add baseline columns to matrix
In particular, -slibase is intended for per-slice modeling of
physiological noise effects. Sucks up a lot of memory and CPU time.
23 Sep 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
save last jumpto_xyz string, etc.
23 Sep 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
in script, check for existence of given datasets
23 Sep 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -remove_preproc_files option (akin to -move_preproc_files)
19 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
-giant_move option
For data that are very far apart
Fixed bug using long path names
18 Sep 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
More options
Intermediate file saved optionally now,
partial_axial,sagittal,coronal options
Edge-based method, nocmass default, resample step optional,
Added options to support searching for smaller structures,
3dWarpDrive can be used optionally as volume registration program
prep_off option to turn off several preprocessing steps
AddEdge option uses simplified names in output in new directory
17 Sep 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 2 (NEW_OPT)
added -labels option, for including labels in filenames
16 Sep 2008, ZS Saad, SurfDist, level 2 (MINOR), type 2 (NEW_OPT)
-node_path_do outputs the shortest path between two nodes
The shortest path(s) are stored as a SUMA Displayable Object
which can be loaded into SUMA with ctrl+alt+s or using DriveSuma.
16 Sep 2008, ZS Saad, DriveSuma, level 2 (MINOR), type 2 (NEW_OPT)
-load_do sends SUMA Displayable Objects to be rendered
See SUMA's interactive help for ctrl+alt+s for more information
on Displayable Objects.
16 Sep 2008, RC Reynolds, 3drefit, level 2 (MINOR), type 4 (BUG_FIX)
allow attribute editing of NIfTI datasets
15 Sep 2008, RW Cox, Draw Dataset plugin, level 2 (MINOR), type 5 (MODIFY)
Keystrokes F3 and F3 now decrement/increment drawing value in plugin
02 Sep 2008, ZS Saad, 3dSkullStrip, level 2 (MINOR), type 4 (BUG_FIX)
Starting sphere center was incorrectly initialized
29 Aug 2008, ZS Saad, ExamineXmat, level 3 (MAJOR), type 1 (NEW_PROG)
An interactive tool to examine a design matrix
29 Aug 2008, ZS Saad, 3ddelay, level 2 (MINOR), type 4 (BUG_FIX)
Uninitialized pointer in 3ddelay
29 Aug 2008, RC Reynolds, vol2surf, level 2 (MINOR), type 5 (MODIFY)
fill in COLMS_STATSYM attribute when writing .niml.dset dataset
29 Aug 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Feature size, AddEdge, skullstrip,rat options
Added options to support searching for smaller structures,
an option for rat brain alignment, alternate options for 3dSkullstrip
and an optional call for @AddEdge
28 Aug 2008, RW Cox, 3dAllineate, level 3 (MAJOR), type 5 (MODIFY)
A number of changes to improve robustness.
* Don't smooth noise added to source image outside of the mask
* Reduce default smoothing level for -lpc in coarse pass
* Increase number of points used for matching in the coarse pass
* More refinements of the twobest results in the coarse pass
* Refinements (-num_rtb option) of the twobest results in the fine pass
All this adds CPU time, but seems to make the program more reliably
convergent. Also:
* Restored operation of the -check option, to restart the optimization
at the final solution with other methods, to see what results they
give compared to the original method.
27 Aug 2008, DR Glen, 3danisosmooth, level 2 (MINOR), type 4 (BUG_FIX)
Initialized variable for 3D case
26 Aug 2008, RW Cox, 3dTcorrMap, level 2 (MINOR), type 1 (NEW_PROG)
Average correlations with every other voxel time series.
Kind of slow. For Kyle Simmons. And I still don't recognize Missouri!
26 Aug 2008, RC Reynolds, 3dAllineate, level 2 (MINOR), type 4 (BUG_FIX)
initialized ntask in all cases
25 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Added residual outputs to 3dREMLfit.
22 Aug 2008, RW Cox, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
Add FDR curves and -?fitts options.
22 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added DRIVE_WAIT command string
The command will be executed after the first volume is processed,
which is good for opening windows appropriate to a new dataset.
21 Aug 2008, RW Cox, 3dREMLfit, level 4 (SUPER), type 1 (NEW_PROG)
Program to mimic 3dDeconvolve, but with serial correlations
Uses ARMA(1,1) model of noise, separately for each voxel.
21 Aug 2008, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
in edt_dsetitems, if storage mode can be inferred from prefix, apply it
21 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 2 (NEW_OPT)
added -disable_done option to safeguard real-time mode
21 Aug 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
use DSET_BRIKNAME for dataset control, as that is updated for smode
18 Aug 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
increase DRIVE_LIMIT to 4Kb, read env vars each run
These variables can now be controlled through drive_afni 'SETENV'
(either via 'plugout_drive' or 'Dimon -drive_afni'):
- AFNI_REALTIME_Mask_Vals : specify what gets sent to serial_helper
- AFNI_REALTIME_SHOW_TIMES : specify whether to show data timestamps
- AFNI_REALTIME_SEND_VER : specify whether to send comm version
15 Aug 2008, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX)
init graph->grid_spacing, to prevent potential div by 0 via DRIVE
14 Aug 2008, RC Reynolds, 3dBrickStat, level 2 (MINOR), type 4 (BUG_FIX)
do not automatically print -max along with -var
05 Aug 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
re-added the un16 fix from July 1
03 Aug 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 5 (MODIFY)
added swap ability for ANALYZE 7.5 format, and made swapping complete
- added nifti_analyze75 struct
- modified swap_nifti_header to swap all fields (analyze or nifti)
- added regression testing script c16.rand.swap
These changes were motivated by C Burns.
03 Aug 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -help_ana, -disp_ana, -swap_as_analyze, -swap_as_nifti, -swap_as_old
31 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 2 to work as -disp_all
See 'HELLO versions' from 'serial_helper -help' for details.
See 'example E' from 'Dimon -help' for a complete testing example.
31 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
enhancements to communication with serial helper
- added 'Motion Only' to methods
- parameter methods can easily be switched per run
- SEND_VER replaces HELLO_VER as Y/N variable
31 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -num_slices option, and full real-time example E
30 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and -show_times option
30 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added HELLO version 1 and show_times option
These are set via AFNI_REALTIME_SEND_VER and AFNI_REALTIME_SHOW_TIMES.
29 Jul 2008, ZS Saad, afni, level 2 (MINOR), type 5 (MODIFY)
Changed transform used to crete mni coord. in interactive whereami
The transform from TLRC to MNI used to be via the manually TLRCed
N27 brain. However this created inconsistency in the second line of the
Focus point output (MNI Brain) on the order of a couple of mm
with the command-line whereami program.
Now both interactive and command-line whereami produce the same
Focus Point output. Note that the rest of the whereami
output remains unchanged.
29 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 5 (MODIFY)
captured and output more signal and error info, flushed output buffer
29 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
print more socket error info, send MP vals w/out mask
28 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 4 (BUG_FIX)
alter check for bad socket: use tcp_alivecheck over tcp_writecheck
28 Jul 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
Pre and post transformation matrices
Allow pre-transformation matrix instead of oblique transformation
and post-transformation instead of tlrc transformation.
Fixed concatenated matrices for oblique data. Master options
allow specification of dimension size on output. Script arguments
saved in output dataset.
25 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
allow -sleep_vol to be very small without early run termination
23 Jul 2008, RC Reynolds, 3dttest, level 2 (MINOR), type 2 (NEW_OPT)
added -base1_dset option, where -base1 value can vary over voxels
Added for M Beauchamp.
18 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
listed signal and noise models in -help output
18 Jul 2008, DR Glen, to3d, level 2 (MINOR), type 5 (MODIFY)
Reverse order of slices in Siemens Mosaic data
Some Siemens Mosaic data can be in reverse order depending upon
obscure Siemens private DICOM tags.
Thanks to Doug Greve in Freesurfer group for edifying this situation
17 Jul 2008, RC Reynolds, 3dNLfim, level 2 (MINOR), type 5 (MODIFY)
warn the user if DSET_NVALS is not the same as DSET_NUMTIMES
That would suggest the dataset has no time axis.
16 Jul 2008, RC Reynolds, serial_helper, level 2 (MINOR), type 2 (NEW_OPT)
added -disp_all to give formatted display of 'all' mask data
This was added for P Kundu.
16 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
added choice of 'Vals to Send' to serial_helper
Can now send index,i,j,k,x,y,z,value for every value in mask.
15 Jul 2008, DR Glen, general, level 2 (MINOR), type 5 (MODIFY)
Can turn off all obliquity warnings
AFNI_NO_OBLIQUE_WARNING variable is extended to turn off warnings
about using oblique data in commandline programs and in GUI
15 Jul 2008, DR Glen, 3dWarp, level 2 (MINOR), type 4 (BUG_FIX)
Print correct obliquity transformation matrix
14 Jul 2008, RC Reynolds, plug_realtime, level 2 (MINOR), type 5 (MODIFY)
terminate TCP transmission to serial_helper if mask is bad
14 Jul 2008, RC Reynolds, afni_history, level 2 (MINOR), type 5 (MODIFY)
a single integer option is interpreted as with -past_entries
14 Jul 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added -sleep_init, -sleep_vol, -sleep_frac
These options control the timeout periods between data checks.
10 Jul 2008, RC Reynolds, plug_realtime, level 3 (MAJOR), type 5 (MODIFY)
receive oblique transform matrix via new OBLIQUE_XFORM interface
10 Jul 2008, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
if the data is oblique, pass the transformation matrix to plug_realtime
01 Jul 2008, RC Reynolds, to3d, level 2 (MINOR), type 4 (BUG_FIX)
fixed crash in case of mosaic and un16, no longer having im data
Problem found by R. McColl.
01 Jul 2008, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 5 (MODIFY)
modified the make system for building programs in the install directory
- modified Makefile.INCLUDE's INFLAGS and ISFLAGS
- modified SUMA_INPATH in SUMA_Makefile_NoDev.
- removed 'rickr/' dirs from includes in mrilib.h, plug_crender.c and
3dAllineate.c
Requested by V. Roopchansingh of MCW.
30 Jun 2008, RC Reynolds, gen_epi_review.py, level 2 (MINOR), type 5 (MODIFY)
make script executable, decrease sleep, add usage comment in script
30 Jun 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added -gen_epi_review and -no_epi_review options
By default, a drive_afni script to review EPI data is now generated.
27 Jun 2008, RC Reynolds, gen_epi_review.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate afni/drive_afni script to review initial EPI data
This program was written to be called from the afni_proc.py output script.
25 Jun 2008, RC Reynolds, howto, level 2 (MINOR), type 5 (MODIFY)
put disclaimers at the tops of HowTo #1, #2, and #5
references to current AFNI class handouts were included
25 Jun 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -past_entries option
24 Jun 2008, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
Extend max number of clusters reportable, for Shruti.
24 Jun 2008, RC Reynolds, 3dDeconvolve, level 2 (MINOR), type 5 (MODIFY)
added the ability to output 1D iresp datasets
20 Jun 2008, RC Reynolds, libmri, level 2 (MINOR), type 5 (MODIFY)
thd_niftiread: do not scale to float if scale=1 and inter=0
19 Jun 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 5 (MODIFY)
help update, added -show_valid_opts, use '*' as separator w/amplitudes
18 Jun 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
Bug fixes - duplicate master options, mislabeled variable
16 Jun 2008, RC Reynolds, file_tool, level 2 (MINOR), type 5 (MODIFY)
show output for multiple bad files when using -show_bad_backslash
13 Jun 2008, RC Reynolds, nifticlib, level 2 (MINOR), type 2 (NEW_OPT)
added nifti_compiled_with_zlib()
13 Jun 2008, RC Reynolds, nifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -with_zlib, and ability to add extensions via 'file:FILENAME'
extension update added for J. Gunter
13 Jun 2008, RC Reynolds, 3dclust, level 2 (MINOR), type 5 (MODIFY)
in the help, Volume defaults to microliters, unless -dxyz=1 is used
12 Jun 2008, RC Reynolds, neuro_deconvolve.py, level 2 (MINOR), type 1 (NEW_PROG)
generate 3dTfitter script to deconvolve a BOLD signal into a neuro signal
11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
Obliquity handling in alignment, more grid options
10 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 2 (NEW_OPT)
Add -ARMA option to estimate ARMA(1,1) parameters
06 Jun 2008, RW Cox, 3dLocalCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, averaged locally.
06 Jun 2008, RW Cox, 3dErrtsCormat, level 2 (MINOR), type 1 (NEW_PROG)
Compute correlation matrix of a time series, globally.
06 Jun 2008, RC Reynolds, plug_crender, level 2 (MINOR), type 4 (BUG_FIX)
integral threshold was off by 1
29 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 5 (MODIFY)
allowed for -polort -1 and for sub-brick selection with dataset names
22 May 2008, RC Reynolds, 3dTshift, level 2 (MINOR), type 4 (BUG_FIX)
with -rlt, slices without any time shift must still be processed
problem noticed by Jie Huang
21 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed incorrect scaling in Cp computation
The error was introduced on April 8, 2008.
20 May 2008, RW Cox, afni, level 2 (MINOR), type 0 (GENERAL)
Clusterize: '-' as the filename means write to stdout.
18 May 2008, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
added options for TR-locking and storing '3dDeconvolve -nodata' examples
- added shuffle() to replace that from random (cannot produce all perms)
- added options -tr, -tr_locked and -save_3dd_cmd
- changed -stim_time option to -stim_dur
17 May 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
check result of 3dDeconvolve execution in output script
If 3dDeconvolve fails, terminate the script so that the user can
see what happened.
15 May 2008, ZS Saad, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
added -n_rand and -n_randseed
15 May 2008, ZS Saad, 3dfim+, level 2 (MINOR), type 4 (BUG_FIX)
Fixed memory corruption when using more than 20 regressors
14 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
fixed application of decay term
14 May 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
1D file names for child epi data,micro changes
13 May 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -set_extern_filelist option, and help for using external data files
13 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
gifticlib-1.0.0: initial release
includes support for (set/clear/read/write) external data files
09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
Added option -1Dformat to output results in 1D format
09 May 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
gifticlib-0.0.18: giiCoordSystem is now an array of struct pointers
modified GIFTI library, along with suma_gifti.c
08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
Fixed memory corruption caused by improper declaration of combName
08 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 5 (MODIFY)
updated help, NFIRST does not need to imply injection time
07 May 2008, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 1 (NEW_PROG)
generate random stimulus timing files
This generates random timing files suitable for use in 3dDeconvolve.
The timing is not restricted to a TR grid, though that is possible.
Consider use with '3dDeconvolve -nodata'.
07 May 2008, RC Reynolds, plug_3Ddump_V2, level 2 (MINOR), type 4 (BUG_FIX)
allow 4D datasets to be opened (so that buckets are again usable)
PLUGIN_dset_check() now checks NVALS instead of NUM_TIMES...
07 May 2008, RC Reynolds, option_list.py, level 2 (MINOR), type 2 (NEW_OPT)
added get_type_list and other accessor functions
01 May 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 4 (BUG_FIX)
treat RESID_CT as Ct(t), not C(t)
30 Apr 2008, RW Cox, mcw_glob.c, level 2 (MINOR), type 3 (NEW_ENV)
setenv AFNI_SHELL_GLOB YES == wildcard expansion via the shell
For Graham Wideman and Mac OS X Server 10.5 problems.
17 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
Child epi datasets can be volume registered even if parent epi
is a single sub-brick
16 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
multiple changes
Naming conventions for tlrc output, generic shell compatible,
regridding options for epi and tlrc epi output
14 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
minor change
3dAllineate options are also applied to epi to anat alignment,
so output EPI datasets get original resolution and type.
10 Apr 2008, DR Glen, align_epi_anat.py, level 2 (MINOR), type 5 (MODIFY)
minor changes
remove tabs in file, change output file names for epi children,
changes to help, and renamed tlrc parent option
08 Apr 2008, RW Cox, 3dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 3D+time dataset (in the time direction)
08 Apr 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 3 (NEW_ENV)
allow residual Ct values via AFNI_MODEL_D3_RESID_CT_DSET dataset
e.g. setenv AFNI_MODEL_D3_RESID_CT_DSET residual_Ct+orig
08 Apr 2008, RC Reynolds, 2dImReg, level 2 (MINOR), type 4 (BUG_FIX)
allow zero slices, passing input as result
Choleski factorization would fail on an empty slice. In this case,
return the input slices as the result (instead of crashing).
Done with D Glen.
07 Apr 2008, RW Cox, 1dUpsample, level 2 (MINOR), type 1 (NEW_PROG)
Upsample a 1D time series
07 Apr 2008, DR Glen, align_epi_anat.py, level 4 (SUPER), type 1 (NEW_PROG)
Alignment of EPI and Anatomical datasets
Aligns anat and EPI data. Alignment is in either direction of anat to
epi or epi to anat. Transformations are combined where possible as
from time series registration and talairach transformations. Multiple
child epi datasets may be aligned at the same time.
04 Apr 2008, RW Cox, 3dAllineate, level 2 (MINOR), type 0 (GENERAL)
Added '-nwarp bilinear' option
Experimental nonlinear warping comes to 3dAllineate at last.
Preliminary test looks good, but more work is needed to be sure it's OK.
02 Apr 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed suma -environment's output to reflect user's current environment.
With this change, users can always replace their .sumarc with
the one output by suma -environment without worrying about losing
their preferred settings.
02 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of contrasts to 75
01 Apr 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
increased internal memory for 3dbucket and 3drefit command creation
31 Mar 2008, RC Reynolds, ANOVA, level 2 (MINOR), type 5 (MODIFY)
extended maximum number of means, diffs and contrasts to 50
28 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -copy_gifti_meta and -copy_DA_meta options
28 Mar 2008, DR Glen, 3dDTeig, level 2 (MINOR), type 4 (BUG_FIX)
small negative eigenvalues are set to zero as in 3dDWItoDT
This fix avoids FA being set to 0 for those affected voxels
27 Mar 2008, ZS Saad, afni-matlab, level 2 (MINOR), type 5 (MODIFY)
Added other return options for Read_1D.m and BrikLoad.m
26 Mar 2008, ZS Saad, cat_matvec, level 2 (MINOR), type 5 (MODIFY)
cat_matvec can now output IJK_TO_CARD_DICOM and IJK_TO_DICOM_REAL
26 Mar 2008, ZS Saad, @SUMA_AlignToExperiment, level 2 (MINOR), type 2 (NEW_OPT)
Added -align_centers as an option to deal with very large moves
It used to be that users had to run @Align_Centers on all their
data when big moves were needed to align the surface's antaomy
to that of the experiment. This is no longer needed.
26 Mar 2008, ZS Saad, @Align_Centers, level 2 (MINOR), type 5 (MODIFY)
Script now outputs a matrix that represents the shift
This matrix can be used with 3dAllineate to perform the shift.
26 Mar 2008, ZS Saad, 3dvolreg, level 2 (MINOR), type 4 (BUG_FIX)
3dvolreg's -1Dmatrix_save was not always accounting for centers of rotation
Now the output of -1Dmatrix_save always matches what one would get for
the first sub-brick from
cat_matvec FRED+orig::VOLREG_MATVEC_000000 -I
26 Mar 2008, RW Cox, 1dplot, level 2 (MINOR), type 2 (NEW_OPT)
Add -norm2 and -normx options: normalize time series before plotting
26 Mar 2008, DR Glen, python, level 2 (MINOR), type 4 (BUG_FIX)
repaired support for dry_run mode in python scripts
25 Mar 2008, ZS Saad, suma-general, level 2 (MINOR), type 5 (MODIFY)
Instead of SAME, one can use surface's name as LocalDomainParent
25 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
ROIs drawn on different surfaces now handled properly
25 Mar 2008, RW Cox, 3dDetrend, level 2 (MINOR), type 4 (BUG_FIX)
-normalize didn't work -- what the hellll was I thinking?
Also, added some help to explain how to use 3dDetrend on 1D files.
25 Mar 2008, RW Cox, 1dnorm, level 2 (MINOR), type 4 (BUG_FIX)
Forgot the sqrt()! kudos to David Perlman.
25 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 5 (MODIFY)
the -compare_data option is not separate from -compare_gifti
25 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
minor changes:
- NIFTI_INTENT_NONE is considered valid
- added compare_gifti_data functions
- LabelTables are now written using CDATA
24 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 5 (MODIFY)
deconvolution with penalty factor = 0 is modified
Now the criterion for choosing the penalty factor is based on curvature
rather than distance from the origin. Seems to be more robust, but
probably will require yet more tweaking.
24 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
added GERT_Reco options (request of D Glen)
-gert_filename : specify a name for the GERT_Reco script
-gert_nz : override nz=1 in mosaic image files
-gert_to3d_prefix : specify a dataset prefix for the to3d command
24 Mar 2008, RC Reynolds, @Align_Centers, level 2 (MINOR), type 4 (BUG_FIX)
applied proper follower dataset orientation and floating point shifts
The shift applied to the child datasets was based on the parent's
orientation. The shifts were also being truncated to integers.
Changed with D Glen.
20 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
Add -polort option, to keep Gang Chen happy.
20 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_WRITE_1D_AS_PREFIX allows writing 1D or surface data given the prefix
For example, setting this to YES will allow writing surface data to NIfTI.
18 Mar 2008, RC Reynolds, gifti_tool, level 2 (MINOR), type 2 (NEW_OPT)
added -compare_gifti option
See 'gifti_tool -help' for details, including example #7.
18 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
added comparison functions to gifticlib
17 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if 1 volume, GERT_Reco_dicom does not give (useless) timing to to3d
13 Mar 2008, RC Reynolds, 3dmerge, level 2 (MINOR), type 0 (GENERAL)
added some examples to the -help output
12 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
Changed surface controller font to 8.
You can get the old font size with environment
variable SUMA_SurfContFontSize BIG.
The default is now SMALL.
11 Mar 2008, RC Reynolds, model_demri_3, level 2 (MINOR), type 2 (NEW_OPT)
added control of hematocrit via AFNI_MODEL_D3_HCT
10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
averages did not include nodes lost to -cmask
Noticed by M Beauchamp.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_GIFTI_VERB sets the verbose level in the gifti I/O library
The default is 1, 0 is quiet, and values go up to 7.
10 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 0 (GENERAL)
AFNI can read/write .gii.dset as with .gii
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
applied -gert_outdir in the case of dicom images
10 Mar 2008, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
if only 1 run, GERT_Reco_dicom is named per run
07 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
Color map in surface controller can be flipped and rotated
* f key for flipping colormap
* Up/Down keys for rotating color map
* Home for home
Hit ctrl+h on Surface Controller's colormap for more help.
07 Mar 2008, RW Cox, Dataset#N, level 2 (MINOR), type 3 (NEW_ENV)
AFNI_DATASETN_NMAX sets number of datasets allowed
New environment variable AFNI_DATASETN_NMAX sets the number of datasets
allowed in Dataset#N plugin, from 9..49. This is for Shruti.
07 Mar 2008, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 4 (BUG_FIX)
properly ignore empty lines, and exit on short files
06 Mar 2008, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
Added three variables affecting the surface controller
* SUMA_ShowOneOnly: Sets '1 Only' on or off. On by default
* SUMA_GraphHidden: Update open graphs even if corresponding dset
is hidden.* SUMA_ColorMapRotationFraction: Fraction of
colormap to rotate
up or down with arrow keys.
See suma -environment for a complete list.
05 Mar 2008, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Support for GIFTI surface format writing
GIFTI writing can now be done with SUMA programs.
For example, see options -o_gii and -xml* in ConvertSurface program.
05 Mar 2008, RW Cox, afni-general, level 2 (MINOR), type 5 (MODIFY)
Change the way 1D datasets are written to disk from 3D programs
In programs that analyze time series files (such as 3dTfitter), you can
input 1D files and make the column direction be the time axis by using
suffixing the file with \' -- but when it comes to writing the results
dataset out, the standard AFNI I/O method is to write the time axis
along the row direction. With this change, if you input a 1D file in
the place of a 3D dataset AND put '.1D' at the end of the output file
prefix, then the output dataset will be written so that the time axis
is along the column direction.
05 Mar 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
added '-fitts' option to produce fitted time series dataset
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 4 (BUG_FIX)
fixed passing of INDEX_LIST
05 Mar 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
do not duplicate data when reading and writing GIFTI from AFNI
04 Mar 2008, RW Cox, 3dDeconvolve, level 2 (MINOR), type 4 (BUG_FIX)
couple of small changes to help the hapless users
* add more informative error message if allocate_memory() fails
* force '-float' if any output prefix is NIfTI-1 format (.nii)
04 Mar 2008, RC Reynolds, 3dTstat, level 2 (MINOR), type 2 (NEW_OPT)
added -accumulate option, to output each partial sum
for k = 0..N-1 : output[k] = sum(input[i]) over i = 0..k
03 Mar 2008, RC Reynolds, website, level 2 (MINOR), type 5 (MODIFY)
updated the AFNI History website pages, with a table of entries
29 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added a TYPE, -type, a new level, and a string to identify each level
29 Feb 2008, G Chen, 3dICA.R, level 4 (SUPER), type 1 (NEW_PROG)
Independent component analysis
This is an R program that runs independent component analysis. It
takes one dataset that presumably has already been properly
pre-processed.already been properly pre-processed. See more details at
https://afni.nimh.nih.gov/sscc/gangc/ica.html
28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
Support for GIFTI surface format reading
28 Feb 2008, RW Cox, 3dUndump, level 2 (MINOR), type 0 (GENERAL)
allow input of NO text files, to produce an 'empty' dataset
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow constraints on sign of deconvolved function
28 Feb 2008, RW Cox, 3dTfitter, level 2 (MINOR), type 2 (NEW_OPT)
allow combination of penalty functions in deconvolution
28 Feb 2008, RC Reynolds, afni_history, level 2 (MINOR), type 2 (NEW_OPT)
added -list_authors option and adjusted spacing
27 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Addition of p and q values under threshold bar
Use BHelp on p and q text in suma to get more info.
27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
add deconvolution via the '-FALTUNG' option
Unlike 3dDeconvolve, this deconvolution is to find the input time
series, given the impulse response function.
27 Feb 2008, RC Reynolds, afni_history, level 4 (SUPER), type 1 (NEW_PROG)
program to display the history of AFNI updates
This will be used to create a web page of AFNI updates.
Please see 'afni_history -help' for more details.
27 Feb 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fixed -regress_use_stim_files typo (was -regress_use_stim_times)
25 Feb 2008, RW Cox, 1dsvd, level 2 (MINOR), type 2 (NEW_OPT)
add '-vmean' and '-vnorm' options, to mirror capabilities in 3dpc
25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
fixed application of cluster for sending data to suma
Previously, clustering was only applied when the Olay and Thr sub-bricks
were the same.
24 Feb 2008, RC Reynolds, GIFTI, level 2 (MINOR), type 5 (MODIFY)
GIFTI library now considers MetaData without Value as valid
22 Feb 2008, RW Cox, 3dpc, level 2 (MINOR), type 2 (NEW_OPT)
add '-eigonly' and '-reduce' options; output eigenvalues to a 1D file
'-eigonly' causes 3dpc to print eigenvalues to stdout and stop there.
'-reduce n pp' outputs a reduced dataset, using only the largest 'n'
eigenvalues.
21 Feb 2008, RC Reynolds, GIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI programs can now read and write GIFTI datasets
GIFTI datasets are for data in the surface domain, with file suffix .gii.
Support must be requested at compile time, and it requires libexpat.
Please see http://www.nitrc.org/projects/gifti for many details.
20 Feb 2008, RW Cox, 1deval, level 2 (MINOR), type 2 (NEW_OPT)
add '-1D:' option, to write output that is usable on the command line
Sample usage:
1dplot `1deval -1D: -num 71 -expr 'cos(t/2)*exp(-t/19)'`
The backquotes `...` capture command's output and put this string on
the command line. The '-1D:' option formats the 1deval output so that
it is ready to be used in this way.
16 Feb 2008, RW Cox, 3dTfitter, level 4 (SUPER), type 1 (NEW_PROG)
new program = linear fits to voxel time series
Uses L1 or L2 regression, with optional constraints to fit each voxel
time series as a sum of basis time series, which can be 1D files or
3D+time datasets. Basis time series that are 1D time series are
the same for all input voxels. Basis time series that are 3D+time
datasets are different for each voxel.
Differences from 3dDeconvolve:
* Basis time series can vary across voxels.
* Fit coefficients can be found with L1 or L2 error functions, and
can be constrained to be positive or negative.
* 3dTfitter does not compute goodness-of-fit statistics.
14 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Graphing of dset content with 'g'
A graph of the column content at a node can be plotted
This would be the surface equivalent to AFNI's graphing function.
See suma's interactive help 'ctrl+h' for more info.
12 Feb 2008, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
An option to show all of suma's environment variables
See help for -environment in suma -help.
06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
Program to calculate geodesic internodal distances
06 Feb 2008, RC Reynolds, 3dbucket, level 2 (MINOR), type 0 (GENERAL)
modified to copy FDR curves
04 Feb 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_NEWSESSION_SWITCH in afni_func.c == switch to new session?
31 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify plug_crender.c to obey AFNI_SLAVE_THRTIME.
24 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add FDR curve generation to 3dANOVA.lib, 3dNLfim, 3dRegana, 3dttest.
* Fix little problems with AFNI threshold scale display as q-value alters.
* Fix bug in thd_mastery.c in assigning FDR curves to mastered sub-bricks.
* Add '-killSTAT' option to 3drefit.
23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* FDR thresh-vs-z(q) curve generation and storage in datasets.
* Display FDR q in AFNI pval label.
* Generate FDR curves automatically in 3dDeconvolve, and with
'-addFDR' option in 3drefit.
22 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dFDR: better help, -float, -qval.
* Add -sort and -SORT options to 3dcalc, for no good reason.
* Add 'help' command to ccalc, to give parser info.
22 Jan 2008, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
added options to estimate smoothness in data for use in AlphaSim
See help options -regress_est_blur_epits and -regress_est_blur_errts.
17 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* AFNI_FLOATIZE environment variable for 3dDeconvolve.c and 3dcalc.c.
* mri_fdrize.c function for FDR-z conversion.
12 Jan 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Scroll lists for I T and B selectors in suma
Right click on pulldown menu titles to get
a scroll list instead. This makes selecting from
a long list of options, or columns, much easier.
Right click on 'I' to the left of suma's Intensity Selection
button for an illustration.
09 Jan 2008, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* SIGQUIT delay in afni.c, for Jerzy.
28 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Popup menu in clusterize report to set histogram range.
28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
program to read and write GIFTI datasets
27 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Upgrades to clusterize reporting window: histograms, from/to indexes
on auxiliary dataset, 3dclust and save table buttons, &c.
* Fixed bug in DG's obliquity reporting function in thd_coords.c -- it
didn't check if the input dataset was valid -- caused AFNI to crash.
20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* Clusterize reporting window.
19 Dec 2007, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
Use of '[i]' to select node index from surface dset
Square bracket '[]' selection works for surface-based
datasets much like it does for volume-based ones.
In addition, one can use '[i]' to select the indices
of nodes for which data are defined in a particular
surface-based dataset.
For more information, see 'SUMA dataset input options:'
section in the output of ConvertDset -help .
18 Dec 2007, ZS Saad, ROIgrow, level 2 (MINOR), type 1 (NEW_PROG)
Grows regions separately, depending on labels
18 Dec 2007, ZS Saad, ROI2dataset, level 2 (MINOR), type 0 (GENERAL)
Output full datasets if needed
17 Dec 2007, ZS Saad, ConvertDset, level 2 (MINOR), type 0 (GENERAL)
Output of full dsets if needed
This can be used to force a dataset with data
defined on a few nodes to be written out with a
complete list of nodes, using 0 where no data are defined.
06 Dec 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add -jpg and -png options to 1dplot.c.
* Add thick line drawing to mri_coxplot.c (by repeated thin line drawing).
03 Dec 2007, RC Reynolds, GIFTI, level 3 (MAJOR), type 0 (GENERAL)
initial release of gifti I/O C API
23 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Modify NI_decode_one_string() in niml_elemio.c to auto-expand buffer
size if string is too long. For festering Lebanese programmers.
* Similarly, modify scan_for_angles() if element header is bigger than
buffer size.
* 'Histogram: Multi' (plug_histog_multi.c) plugin, for Kyle, Alex, & Pat.
20 Nov 2007, RW Cox, 3dTsort, level 3 (MAJOR), type 1 (NEW_PROG)
new program = sorts voxel data along the time axis
This might be useful for sorting the -stim_time_IM beta weights
output be 3dDeconvolve. Perhaps for something else, too?
20 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 1 (NEW_PROG)
Older History stuff
* Copy auxdata from source to output in 3dAllineate.c (oops).
* Changed 'report' from mri_clusterize.c and added info to the
clusterize vector chooser using about BHelp to see this report.
* New program 3dTsort.c. Will this grow to be a monster?
19 Nov 2007, ZS Saad, Surf2VolCoord, level 2 (MINOR), type 1 (NEW_PROG)
Program to show surface-node to voxel correspondence
This can be used to understand how surface coordinates
relate to voxel coordinates.
16 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Added -global_times, -local_times, and -guess_times to 3dDeconvolve.c
* For ragged 1D input files, arbitrary text starting with alphabetic
character is same as '*' for filler.
* AFNI_RESCAN_AT_SWITCH is on by default now.
* 1dplot takes a 1 row file and flips it to a column for plotting; however
,
when 2 single row files were input, they'd be catenated and THEN
flipped, producing erroneous joined plot. Now, they are flipped
THEN catenated, which does the right thing.
* Speaking of 1dplot, '-nopush' now works for multiple graphs, rather
than just for '-one'.
* Modify AlphaSim.c so that rmm defaults to -1 ==> nearest neighbors,
and so that '-seed 0' generates a custom seed.
* Add some extra text to the 'Clusterize' label (afni_setup.c) to
explain that rmm=0 means NN clustering with vmul in voxel count.
15 Nov 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to interactive AFNI to save '1D:' ref and ort files in the
header of interactive fim files; example
1dplot '`3dAttribute -ssep ' ' AFNI_FIM_REF r1_time@1+orig`'
* Changes to mri_read_1D() to allow arbitrarily long filenames.
* New function mri_1D_tostring(), to create '1D:' strings from MRI_IMAGEs.
(see file mri_fromstring.c)
12 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Changes to bbox.c to add an arrowval index selector to the single-select
ion
mode strlist chooser (per Shruti Japee's unreasonable demand).
11 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify edt_filtervol.c to clip off voxels outside the fmask.
* Modify 3dmerge.c to add -1fm_noclip and -1filter_blur options.
10 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve.c to check -stim_label values: for un-assigned
values, and for duplicate values.
* Change a few programs to check EQUIV_GRIDS() as well as voxel counts,
when combining multiple datasets (3dTcat, etc).
* Modify plug_nth_dataset.c to use different set of default overlay colors
.
Modify afni_plugin.[ch] to allow this.
* Modify afni_graph.c to make 'Transform 1D' menu re-activate a button eve
n
if it is already the activated one. Goal: popup Dataset#N plugin
controls more easily.
* Modify 3dttest.c to add the -sdn1 option (for Tom Johnstone).
04 Oct 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify afni_graph.c to turn Double Plot on when Dataset#N is invoked,
and to not double plot transformed time series that didn't change.
* Print 'NFirst > 0' informational message in 3dDeconvolve.c.
* Change OPACITY_BOT from 0 to 1 in imseq.c.
26 Sep 2007, ZS Saad, SurfFWHM, level 4 (SUPER), type 1 (NEW_PROG)
Program to estimate FWHM of data on surface
26 Sep 2007, ZS Saad, SurfSmooth, level 3 (MAJOR), type 5 (MODIFY)
Big changes to data smoothing functions
* HEAT_07 method does controlled blurring, with options
to blur 'to' a particular FWHM. No guessing needed for
iterative kernel bandwidth or number of iterations.
* HEAT_05 method improved to reduce numerical precision
problems.
20 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add '-allcost' options to 3dAllineate.c and mri_genalign.c.
* Neuter program 3dAcost.c.
* Environment variable AFNI_INDEX_SCROLLREV.
20 Sep 2007, G Chen, 3dLME.R, level 4 (SUPER), type 1 (NEW_PROG)
An R program for linear mixed-effects analysis at group level in AFNI
See more details at https://afni.nimh.nih.gov/sscc/gangc/lme.html
18 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'RGB:r,g,b' format to DC_parse_color() in display.c.
* Fixed some bugs in 'Clipped' display.
17 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Clipped' option to image grayscaling, in imseq.c and afni.c.
12 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'All AFNI Splashes' button to 'hidden' menu, just for fun.
10 Sep 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Minor changes to 3dAllineate.c: '-autoweight**1.5' sub-option;
'-autoweight' now the default for '-ls' cost function.
* Re-insert older fixes to afni.c that were lost in CVS.
31 Aug 2007, RC Reynolds, DECONFLICT, level 3 (MAJOR), type 5 (MODIFY)
modified default behavior of programs from deconflict to no overwrite
See AFNI_DECONFLICT in README.environment.
31 Aug 2007, RC Reynolds, model_conv_diffgamma, level 2 (MINOR), type 1 (NEW_PROG)
NLfim model to compute the convolution of the difference of gammas
20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
Older History stuff
* First version of '-lpc' Local Pearson Correlation cost function in
3dAllineate.c, with rhombic dodecahedra as the default building bloks.
14 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Modify 3dDeconvolve.c to allow 'POLY' model to have order up to 20.
* Modify 3dLocalBistat.c to allow '-weight' option for '-pearson' statisti
c.
08 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Add threshold signage feature to AFNI threshold menu ('Pos & Neg', etc).
03 Aug 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_SEE_OVERLAY environment variable.
* Turn overlay on when user first-time switches Overlay, and turn TTatlas
colors on when user pops up atlas color chooser panel.
31 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 2 (NEW_OPT)
Older History stuff
* Make -cmass the default in 3dAllineate.c.
* Also add '+clip' feature to '-autoweight' in 3dAllineate.c.
30 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_read_vecmat.c to use mri_read_double_ascii() to read a file r
ather
than read it directly. This way, comments will be skipped properly and
the '1D: ...' format can be used.
* Fix afni_plugin.c to initialize loading of matrix_initialize(), to fix a
problem left in plug_deconvolve.c by RCR's matrix.c changes.
* Matrix square root in mri_matrix.c, and thence to 1dmatcalc and cat_matv
ec.
30 Jul 2007, RC Reynolds, regression_tests, level 3 (MAJOR), type 0 (GENERAL)
added setup for regression testing to NIFTI package
This can be used as a template for testing any command-line programs.
27 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add 'SPMG3' to 3dDeconvolve.c.
* Fix bug in -1Dmatrix_save in 3dAllineate, when dealing with zero-padded
base.
25 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dAllineate, 3dvolreg, and 3dWarpDrive to output base-to-source m
atrices.
* Modify cat_matvec to deal with files of multiple matrices.
* Modify 3dAllineate to make '-clbin 0' the default.
* Modify afni to add an AutoThreshold button to the threshold popup menu.
16 Jul 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -stim_times_IM to 3dDeconvolve.c, to get individual event amplitudes
.
29 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Boxed plots work with Dataset#N now, in glorious colors and thinned.
But not with Double Plot.
28 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Threshold on/off in reactivated thr_label popup menu in Define Overlay.
* -x1D_stop in 3dDeconvolve.
26 Jun 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Boxed plots in afni_graph.[ch]. Probably a can of worms.
25 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dDeconvolve and 3dSynthesize so that censored time points
can be reconstructed in some fashion in the latter program.
* -x1D_uncensored in 3dDeconvolve.
06 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify thd_writedset.c to always do THD_deconflict_prefix(), unless told
not to by AFNI_DONT_DECONFLICT. Modify a bunch of 3d programs to NOT
check for filename conflict on output.
* Modify thd_correlate.c build_2Dhist() to avoid histogram overflow (oops)
.
05 Jun 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dBlurToFWHM.c and 3dFWHMx.c to use detrending.
* Add THD_patch_dxyz_* functions to thd_auxdata.c, to make sure MRI_IMAGE'
s
in a dataset have the correct dx,dy,dz fields.
30 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve mmap() usage to include MAP_NORESERVE flag.
* Add -allzero_OK option to 3dDeconvolve.c.
* Make 3dttest check for duplicate dataset filenames.
09 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New advanced histogram options '-clbin' and '-eqbin' for 3dAllineate.
04 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 'amongst' function in parser.f and so in 3dcalc.c.
* Added more warnings to 3dDeconvolve.c, including a parametrized -GOFORIT
.
03 May 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'crop=' to afni_driver.c image window opening, and also to afni_sp
lash.c
when saving .afni.startup_script file. [Per John Butman]
* Modified 3dDeconvolve.c to print clearer messages when -gltsym errors
occur, and also to allow the Decon -bucket dataset to be overwritten,
and also to add the -nobucket option. [Per Mike Beauchamp]
30 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Included 3dinfo.c patch from Colm Connolly with -label2index option.
26 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify imseq.[ch], afni.c, and afni_graph.c to use '[' and ']' keys for
time index incrementing, per John Butman.
04 Apr 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDespike.c to add -localedit option.
* Modify 3dAllineate.c to save matrices into header of output.
26 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Moved on-the-fly cluster editing to Define Overlay panel, from popup men
u.
23 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New function THD_deconflict_prefix() in thd_opendset.c.
* Modify 3dDeconvolve.c to deconflict output prefixes (instead of failing)
,
and to compute Full F by default, unless -nofullf_atall is given.
* AFNI_IMAGRA_CLOSER, for the FC5 abusers out there.
21 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 3dEmpty.c.
* Fix 3dinfo.c to allow empty datasets (duh).
16 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -polort A and polort degree warning message.
* Change CTENT() to CSPLIN().
15 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added CTENT() to 3dDeconvolve.c, for experimental purposes.
* Modified bucket labels in 3dDeconvolve.c to be clearer (to me, anyhoo).
14 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 1dMarry.c.
13 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Minor changes to 3dSynthesize.
* Change PRINT_VERSION() macro in mrilib.h to include compilation __DATE__
in output.
* '-float' option to 3dDeconvolve. Also a few little other fixes.
12 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dSynthesize.c.
10 Mar 2007, ZS Saad, MapIcosahedron, level 2 (MINOR), type 5 (MODIFY)
Better handling of surface centers
09 Mar 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* First test of -stim_times_AM? looks good.
* MCW_discard_events() for Button4/5 ScrollWheel actions.
07 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dDeconvolve.c: -GOFORIT, check_matrix_condition(), report -stim_times
values outside of run intervals, condition numbers with and without
baseline regressors.
05 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -nfft and -detrend options to 3dDFT.
* Added 'u' and 'o' image viewer keypress handling to afni.c.
* Added Mod+Button4+5 threshold slider changing to imseq.c and afni.c.
* Added AFNI_THRESH_AUTO to afni_func.c.
01 Mar 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add dilation to -automask option in 3dAllineate. And -ignout option.
* Add -CENSOR to 3dDeconvolve.c.
27 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 3 (NEW_ENV)
Older History stuff
* AFNI_DISABLE_TEAROFF environment variable.
21 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified Edit Environment pseudo-plugin (afni_pplug_env.c) to sort
controls by variable name.
* Added 'instant switch on selection' mode to 'Overlay' and 'Underlay'
dataset choosers, controlled by AFNI_DATASET_BROWSE variable.
* And to 'Talairach To' controls.
* Fixed bug when '-R' would fail to find any datasets, and would then
try to reconcile parents, look for duplicates, etc., de-referencing
NULL pointers. Not sure what happened, actually, but one technique
was to avoid trying to read directories as regular file datasets.
18 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* When running 'afni' (no directory args) and no data is found is './',
then afni.c will now recurse 1 level on './' to see if any datasets
can be found 1 level deeper. Inspired by Korea workshop and Hame Park.
15 Feb 2007, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
High resolution image saving with ctrl+r
Very high resolution images can be created.
See suma's interactive help 'ctrl+h' for more info.
05 Feb 2007, ZS Saad, SurfDsetInfo, level 2 (MINOR), type 1 (NEW_PROG)
Program to display surface dataset information
Output is crude at the moment.
02 Feb 2007, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added a 'Rescan' button next to 'Overlay' and 'Underlay' in the main
AFNI controller. At the demand of Ziad Saad.
* Later: and a 'NIML+PO' button below that.
17 Jan 2007, G Chen, 1dSEM, level 4 (SUPER), type 1 (NEW_PROG)
Path analysis (or structural equation modeling) at group level.
See more details on: https://afni.nimh.nih.gov/sscc/gangc/PathAna.html
15 Jan 2007, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
Allow replacement of pre-loaded DO and Dsets
When a dataset is reloaded, it replaces the one
already loaded in suma.
05 Jan 2007, ZS Saad, imcat, level 2 (MINOR), type 1 (NEW_PROG)
Program to stitch images.
20 Dec 2006, RC Reynolds, afni_proc.py, level 4 (SUPER), type 1 (NEW_PROG)
program to write complete single subject FMRI processing script
14 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added SAVE_FILTERED to the roster of AFNI driver commands.
11 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* More changes to 3dBlurToFWHM.c -- de-median and de-MAD before blurring a
nd
before estimating blur, to be somewhat more self-consistent.
* Added SAVE_PNG to the roster of AFNI driver commands.
11 Dec 2006, RC Reynolds, make_stim_times.py, level 2 (MINOR), type 1 (NEW_PROG)
program to convert stim_files to stim_times files
08 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -dem option to 1ddot.c.
07 Dec 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added movie saving commands to afni_driver.c.
* Modified 3dFWHMx.c -geom option to add up logs rather than multiply up
results -- for large numbers of sub-bricks, can get overflow the old wa
y.
* Added THD_medmad_bricks() and THD_meansigma_bricks() functions to
thd_median.c -- get location and dispersion statistics at same time,
for speed.
30 Nov 2006, ZS Saad, suma, level 2 (MINOR), type 0 (GENERAL)
Addition of new Displayable Objects (DO)(ctrl+Alt+s)
Allows display of segments, spheres and other markers
See suma's interactive help 'ctrl+h' for more info.
20 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Multitudinous changes to 3dBlurToFWHM.c.
15 Nov 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dBlurToFWHM.c.
09 Nov 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dFWHM to do what 3dFWHMx does -- not use a voxel in a differen
ce
unless it is in the mask as well.
31 Oct 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* New program 3dFWHMx -- does all sub-bricks.
30 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified plug_scatplot.c to copy 'Aboot' option from plug_histog.c.
* Modified THD_pearson() stuff in thd_correlate.c to remove mean.
* New program 3dLocalBistat.c -- joint local statistics between 2
datasets.
24 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dAutomask.c (etc.) to add -peel and -nbhr options, with
also a fix to stupid error made a couple days before.
22 Oct 2006, RC Reynolds, model_demri_3, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model for Dynamic Enhanced MRI
12 Oct 2006, RC Reynolds, serial_writer, level 2 (MINOR), type 1 (NEW_PROG)
program to send data from a file, pipe or made up to a given serial port
10 Oct 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dClipLevel.c to allow float input datasets.
* Modified 3drefit.c to make '-TR' option add a timeaxis to a non-3D+time
dataset.
* More changes to 3dAllineate.c.
* Program 3dAcost.c to compute 3dAllineate costs on 2 bricks [now gone].
29 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* 3dAllineate.c edited to make -linear the default interpolation during
alignment process, and -cubic for the output dataset.
27 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified correlation ratio in thd_correlate.c to use both Var(y|x) and
Var(x|y) for symmetry between base and target. Seems to make
registration work better.
* Added -check and -master options to 3dAllineate.c.
21 Sep 2006, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Put 3dAllineate into the distribution. But is not finished.
* Modified plug_nlfit.c to allow AFNI_NLFIM_METHOD to select optimizer.
20 Sep 2006, ZS Saad, DriveSuma, level 3 (MAJOR), type 1 (NEW_PROG)
Program to control SUMA from the command line
05 Sep 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Mod mri_read_1D() so that ending filename in ' character causes
transposition. Removed this feature from thd_1Ddset.c to match.
* Changes to AFNI to allow on-the-fly cluster editing.
14 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add pairmax() to parser.f.
08 Aug 2006, RC Reynolds, C++, level 2 (MINOR), type 5 (MODIFY)
afni program compiles in C++ (effort with Rich and Greg Balls)
04 Aug 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add max displacement to 3dvolreg.c.
03 Aug 2006, RC Reynolds, NI_SURF_DSET, level 4 (SUPER), type 0 (GENERAL)
added a new surface dataset format, with read/write ability in AFNI
24 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* model_linplusort.c (Linear+Ort) for 3dNLfim.c.
18 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Fixed -xyzsave option in 3drefit.c to make multiple datasets match.
17 Jul 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added options -keepcen and -xyzscale to 3drefit.c.
24 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -sum option to 3dTstat.c.
10 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -polort option to 3dDetrend.c.
05 Apr 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -frugal option to 3dZcat.c.
31 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* to3d.c: if first filename is 'something.img', check if 'something.hdr'
exists, and if so, suggest that the .hdr file is more likely to be
what they want to input.
* Added '-method' and smoothing options to 3dInvFMRI.c.
29 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* First version of 3dInvFMRI.c.
28 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dDeconvolve.c to set ival=-1 on various inputs, before
sscanf()-ing it, so that bad values give error messages.
* Also add -x1D option to 3dDeconvolve.c, to save X matrix to a .1D file.
20 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modify 3dAutomask.c and thd_automask.c to add new -clfrac option.
* Modify matrix_f.c to use Solaris BLAS in single precision.
13 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Checks in afni_func.c, adwarp.c, and thd_writedblk.c for free disk
space, just before actual writing of .BRIK file.
* 3dTwotoComplex.c from 3dThreetoRGB.c
10 Mar 2006, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Mods to 3dcalc.c to allow use of complex-valued dataset on input.
25 Jan 2006, RC Reynolds, model_michaelis_menton, level 3 (MAJOR), type 1 (NEW_PROG)
NLfim model function for ethanol studies
06 Dec 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -coarserot in 3dWarpDrive.c, too.
02 Dec 2005, RC Reynolds, ANOVA, level 5 (SUPERDUPER), type 5 (MODIFY)
changed variance computations in 3dANOVA programs to not assume sphericity
For details, see https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html .
01 Dec 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -coarserot in 3dvolreg.c
01 Dec 2005, G Chen, 3dANOVA3, level 3 (MAJOR), type 2 (NEW_OPT)
New options to run 2nd-order general linear contrasts in 3dANOVA3.
See more details on: https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
29 Nov 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Message of the Day (motd) stuff.
18 Oct 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -usetemp option to 3dcalc.c.
* Added some timing delays to popup/popdowns.
11 Oct 2005, RC Reynolds, 3dmaxima, level 3 (MAJOR), type 1 (NEW_PROG)
command-line version of maxima plugin
28 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Changes to 3dWarpDrive.c to summarize results (-summ) and to prevent ste
ps
that make the RMS error much worse.
23 Sep 2005, G Chen, 3dANOVA2 and 3dANOVA3, level 4 (SUPER), type 4 (BUG_FIX)
Significant modifications in 3dANOVA2 and 3dANOVA3
The changes were made to avoid statistics inflation for general linear
contrasts when coefficients don't add up to 0. See more details at
https://afni.nimh.nih.gov/sscc/gangc/ANOVA_Mod.html
21 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified thd_writedset.c and 3dAFNItoNIFTI.c so that if AFNI_AUTOGZIP is
YES, then .nii.gz files will be written instead of .nii files.
01 Sep 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Fixed 3drotate.c so that '-rotate 0 0 0' doesn't fail.
23 Aug 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* -FILE option for waver.c.
* In imseq.c: 's' (sharpen), 'D', 'M', 'S' (Disp, Mont, Save).
22 Aug 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* New program 3dLocalstat.
* In imseq.c: 'm' (toggle Min-to-Max), 'a' (fix aspect), 'l' (LR mirror).
* '%s' in thd_compress.h means that you can now read .gz files with spaces
in their names.
15 Aug 2005, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* From now on, unless AFNI_ALLOW_MILLISECONDS is set to YES, AFNI programs
will
convert MSEC time unit datasets to SEC on input and output.
29 Jul 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added '-com' option to afni.c.
* Added grapher windows to SAVE_JPEG in afni_driver.c.
28 Jul 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added stuff to afni_driver.c (SAVE_JPEG, SET_DICOM_XYZ, SET_SPM_XYZ,
SET_IJK, SET_XHAIRS), and imseq.[ch].
05 Jul 2005, RC Reynolds, Dimon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor real-time acquisition of DICOM images
06 Jun 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Brodmann Areas' image popup to the 'Hidden' popup menu.
24 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add 'i' and 'I' keystrokes to afni_graph.c, to move init_ignore down/up.
17 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Draw ROI plugin' menu item to image viewer popup, in afni.[ch].
13 May 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'xamplitude' option to waver -tstim option.
* Oops. Fixed bug in 3dDeconvolve for -iresp/-sresp options: malloc-ed
the 'hout' float** array with sizeof(float) not sizeof(float*), which
doesn't work too good on 64 bit systems.
* Modified 1dplot.c to
(a) allow reading up to 10000 numbers on a line from stdin, and
(b) transpose input file if it has only 1 line, so that a long
single line of numbers becomes a decent plot.
28 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve to add -basis_normall option, and a couple of
other minor tweaks.
27 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dDeconvolve.c to allow -stim_times to be used with -nodata.
To do this, you use '-nodata NT TR' to specify the number of time
points and their TR.
* Modified imseq.c to make up/down movement of stroking affect RGB,
additively, much as left/right does multiplicatively.
25 Apr 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
AFNI can read and write NIFTI datasets (effort with Bob and Rich)
20 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified afni_func.c to let 0 values in the overlay image get color
if environment variable AFNI_OVERLAY_ZERO is set to YES.
15 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -automask option in 3dDeconvolve.c.
* Add mri_write_jpg() to mri_write.c. Now mri_write() automatically
writes a .jpg file for RGB and BYTE images if the filename ends
in '.jpg'.
06 Apr 2005, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* Added '.nii' output feature to THD_writedset() function, and did
a few other similar things hither and yon.
04 Apr 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added 'Pleg' function to parser and thence to 3dcalc, etc.
22 Mar 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* mean(), stdev(), and sem() for parser and 3dcalc.
* Modify Ziad's plugout_drive.c '-com' option to execute commands in
order given, rather than the reverse order.
* Fix REDISPLAY in afni_driver.c (oopsie).
* Added '' input to afni_niml.c, to store as .1D files.
* Added '-Dname=val' option to afni.c (set environment variables).
08 Mar 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Including retroicor stuff from Fred Tam.
25 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Add -min option to 3dmaskave.c.
* Fixed memory leak in niml_dtable.c (forgot to free second copies of stri
ngs).
* New niml_registry.c stuff, for allocating 'registered' structs.
24 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dmaskave.c to have -max option.
* Modified niml/ functions to generalize NI_group elements so that any
element name is OK, provided attribute ni_form='group' is present.
22 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dTshift.c and to3d.c to have new 'alt+z2' option.
* New program 3dMedianFilter.
* Added I:*.1D stuff to 3dcalc.c.
18 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified afni_driver.c, imseq.c, and afni_graph.c to add 'keypress='
modifiers to the OPEN_WINDOW commands for driving AFNI.
16 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified 3dhistog.c to remove -thr stuff and add -doall stuff.
01 Feb 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -redo_bstat option to 3drefit.c.
24 Jan 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added environment variable AFNI_SLAVE_THRTIME to afni.c.
14 Jan 2005, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added program whereami, from Mike Angstadt of U Chicago.
07 Jan 2005, RC Reynolds, nifti_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to directly manipulate or compare NIFTI dataset headers
07 Jan 2005, RC Reynolds, NIFTI, level 4 (SUPER), type 0 (GENERAL)
initial release of NIFTI library
22 Dec 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Incorporated 3dMean.c changes from Mike Beauchamp to add standard deviat
ion
option.
* Fixed stupid scale_thr bug in afni_func.c.
01 Dec 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added -twopass option to 3dWarpDrive, etc.
30 Nov 2004, RW Cox, Miscellaneous, level 3 (MAJOR), type 0 (GENERAL)
Older History stuff
* First version of 3dWarpDrive released.
* 3dcalc now prints a warning if outputting a byte-valued dataset when the
calculated results had some negative values.
21 Oct 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Also added ISPOSITIVE and ISNEGATIVE functions to parser.f
20 Oct 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified parser.f to add NOTZERO, ISZERO, and EQUALS functions.
04 Oct 2004, RC Reynolds, vol2surf, level 4 (SUPER), type 0 (GENERAL)
added vol2surf interface for real-time mapping from afni to suma
29 Aug 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added EXPR(bot,top) basis function to 3dDeconvolve.c.
29 Jul 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Added mri_symbolize.c, and -gltsym option to 3dDeconvolve.
27 Jul 2004, G Chen, PathAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package that runs group analysis of up to 5-way ANOVA
This package adopts the conventional ANOVA approach to handling gorup
analysis. And it requires Statistics Toolbox other than the basic Matlab.
See more details on: https://afni.nimh.nih.gov/sscc/gangc
27 Jul 2004, G Chen, IndiAna, level 4 (SUPER), type 1 (NEW_PROG)
A Matlab package for individual subject analysis
See more details at https://afni.nimh.nih.gov/sscc/gangc
21 Jul 2004, RW Cox, Miscellaneous, level 2 (MINOR), type 0 (GENERAL)
Older History stuff
* Modified MCM_get_intlist() to print error messages when the user inputs
values off the top end of the range, instead of silently turning them
into the top (stupid users).
* Modified afni_fimmer.c to correctly use scaling factors if present in
the time series data (oops, for about 8 years).
* Added printout of pseudo-inverse to 1dsvd.c.
* Added -svd option to 3dDeconvolve. Also, if SVD is on, then DON'T
remove all zero stimuli from the list.
* Added -xjpeg option to 3dDeconvolve: grayplot of X matrix.
31 Mar 2004, RC Reynolds, serial_helper, level 3 (MAJOR), type 1 (NEW_PROG)
program to pass realtime registration params from TCP to serial port
01 Dec 2003, RC Reynolds, SurfMeasures, level 3 (MAJOR), type 1 (NEW_PROG)
program to compute various measures over surfaces
05 Aug 2003, RC Reynolds, 3dVol2Surf, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the volume to domain to the surface domain
29 May 2003, RC Reynolds, 3dSurf2Vol, level 4 (SUPER), type 1 (NEW_PROG)
program to map data from the surface domain to the volume domain
15 Jan 2003, RC Reynolds, Imon, level 3 (MAJOR), type 2 (NEW_OPT)
added connection to the realtime plugin in afni
27 Nov 2002, RC Reynolds, Imon, level 4 (SUPER), type 1 (NEW_PROG)
program to monitor GE I-files as they are written to the scanner
01 Oct 2002, RC Reynolds, file_tool, level 4 (SUPER), type 1 (NEW_PROG)
program to perform generic manipulations of binary files
20 Jun 2002, RC Reynolds, @make_stim_file, level 2 (MINOR), type 1 (NEW_PROG)
script to create binary stim files
06 Jun 2002, RC Reynolds, @SUMA_Make_Spec_FS, level 3 (MAJOR), type 1 (NEW_PROG)
script to import FreeSurfer surfaces into SUMA
21 May 2002, RC Reynolds, 3dresample, level 4 (SUPER), type 1 (NEW_PROG)
program to change a dataset orientation and/or grid spacing
08 Mar 2002, RC Reynolds, plug_crender, level 4 (SUPER), type 1 (NEW_PROG)
added rendering plugin to afni
16 Jan 2001, RW Cox, AFNI-general, level 5 (SUPERDUPER), type 0 (GENERAL)
Older History stuff
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== This was the day I (RWC) started working at the NIH! :) ==
== All changes from this date onwards were made at the NIH ==
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24 Jul 1996, RW Cox, Miscellaneous, level 5 (SUPERDUPER), type 0 (GENERAL)
Oldest History stuff
AFNI was created in summer 1994 (but some parts date to the 1980s).
However, no formal log was made of changes until this date in 1996.
So this is the beginning of AFNI historiography.
'Lately it occurs to me: What a long, strange trip it's been.'
auto-generated by afni_history on Dec 17 2024