AFNI HISTORY
level 1 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 1 -past_years 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
17 Nov 2024, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
use xcode 15.1 in .circleci/config.yml
Version 14.2 was too old (macos 12), and 15.3 has proto issues to fix.
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
30 Aug 2024, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 6 (ENHANCE)
mark linux_xorg7 and linux_xorg7_64 as being obsolete
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
07 May 2024, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
3dCM briefly required a mask
Thanks to P Kundu for pointing out the problem.
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
12 Apr 2024, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 6 (ENHANCE)
add an AFNI ID to the resulting SurfVol, for afni/suma communication
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
04 Apr 2024, RC Reynolds, Surf2VolCoord, level 1 (MICRO), type 6 (ENHANCE)
add a detailed help example for distance to a restricted set of coords
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.
07 Mar 2024, RC Reynolds, abids_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
use compare_py_ver_to_given() for comparison of python versions
Also, removed a few similarly problematic float comparisons.
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.
23 Feb 2024, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE)
sync crorden/dcm2niix_console with repo, version v1.0.20240202
Thanks to C Rorden for the update.
23 Feb 2024, RC Reynolds, @radial_correlate, level 1 (MICRO), type 6 (ENHANCE)
fail if no corr dset (check, since script is not run with -e)
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
20 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 1 (MICRO), type 4 (BUG_FIX)
forgot to actually print out the computed depth
Thanks to P Taylor for noticing.
20 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
remove irritating -script and -out_dir opts, just use subject ID
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.
15 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
remove 2 warnings
No warn on dupe followers if grids are the same; no ACF warning.
14 Feb 2024, DR Glen, whereami, level 1 (MICRO), type 2 (NEW_OPT)
whereami -index_to_label to show label for an index
Labels can be from ordinary labeltabled ROI datasets
or from atlas datasets
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.
07 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
allow underscores in example names, and convert to spaces
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.
05 Feb 2024, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
change GIFTI write from PREFIX to HEADNAME
Previously, the output directories were not being used.
Thanks to eriklee (AFNI MB) for noting the problem.
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
19 Jan 2024, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY)
have wrap_file_text() default to wrap=2 in nwrite_text_to_file()
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.
02 Jan 2024, RC Reynolds, init_user_dotfiles.py, level 1 (MICRO), type 6 (ENHANCE)
apply apsearch updates only if shell file applies to current or login
02 Jan 2024, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
warn on matplotlib version 3.1.2 for not being able to write JPEG
22 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
get a new idcode whenever a new dataset name is assigned
This deals with programs like 3dTsplit4D creating multiple datasets,
as well as programs like afni reading many similarly named files
Thanks for J Blujus for reminding of the issue.
21 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
allow nim->nvox to exceed int32_t range with NIFTI-1 output
Thanks to P Rais-Roldan for noting the discrepancy.
21 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT)
add AFNI_NIFTI_WRITE_TYPE to override choice of NIFTI-1 or -2 output
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
22 Sep 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
in examples, change MNI152_T1_2009c+tlrc to MNI152_2009_template.nii.gz
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.
15 Sep 2023, RC Reynolds, init_user_dotfiles.py, level 1 (MICRO), type 6 (ENHANCE)
in .zshrc, pass -i to compinit, to ignore insecure files
Whines from compaudit: files not owned by root or user or with perm g+w.
Done with D Glen.
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.
28 Aug 2023, RC Reynolds, build_afni.py, level 1 (MICRO), type 5 (MODIFY)
apply renamed test_afni_prog_help.tcsh program
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.
16 Aug 2023, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE)
sync crorden/dcm2niix_console with repo, version v1.0.20230411
Thanks to C Rorden for the update.
16 Aug 2023, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE)
turn off local signing in crorden/dcm2niix_console/makefile
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.
24 Jul 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
if -tlrc_NL_warped_dsets, require -tlrc_base
Require user to verify which template was used to make warped dsets.
Requested by D Glen.
21 Jul 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
fix help for -regress_make_corr_vols
It WAS ave corr, but as of Jan 2020, it is corr of voxels vs ave.
Thanks to D Glen for noting the discrepancy.
19 Jul 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX)
fix use of min instead of minor
Thanks to @dojoonyi for letting us know.
26 Jun 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
write NIFTI-2 if dimensions require it
22 Jun 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
pass tlrc_base uvar as template
Sorry, PT.
20 Jun 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
under linux, check for shared dependencies of R_io.so
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
08 Jun 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
turn off check for PyQt4
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.
12 May 2023, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
R-3.6.3.nn.pkg has been moved to cran-archive.r-project.org
Thanks to Sally D for letting us know.
12 May 2023, RC Reynolds, Makefile.macos_13_ARM_clang, level 1 (MICRO), type 5 (MODIFY)
comment out EXTRA_INSTALL_FILES
Might vary, and is not needed for non-distribution system.
10 May 2023, RC Reynolds, Makefile.macos_12_x86_64, level 2 (MINOR), type 2 (NEW_OPT)
add Makefile, updates, and OS_notes
05 May 2023, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
distribute prog_list.txt (and _bin and _scripts)
Later we will (modify) and distribute test.afni.prog.help, perhaps.
05 May 2023, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX)
fix error cur_afni error if no AFNI is present
This was failing to finish setting up dot files.
02 May 2023, RC Reynolds, RetroTS.py, level 1 (MICRO), type 5 (MODIFY)
numpy.complex() is deprecated, use complex()
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.
25 Apr 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
note possibly using the regress block in -radial_correlate_blocks
This might be particularly useful with ANATICOR.
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.
08 Feb 2023, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
give error message when image writing fails on missing external program
Warn on missing programs cjpeg and pnmtopng
07 Feb 2023, RC Reynolds, @RetinoProc, level 1 (MICRO), type 5 (MODIFY)
as with afni_proc.py, get SurfSmooth parms from smrec file
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.
11 Jan 2023, P Taylor, @chauffeur_afni, level 1 (MICRO), type 6 (ENHANCE)
Extra check of a couple of options, that only correct key words are used.
Done for the '-left_is_* ..' opts.
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
auto-generated by afni_history on Dec 17 2024