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 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
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 wanings 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
16 Dec 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
update mask order in examples 6,6b (mask then blur)
09 Dec 2022, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
add more detail to afni_system_check.py -help_dot_files
07 Dec 2022, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE)
add more detail to timing_tool.py -help_basis
06 Dec 2022, P Taylor, @chauffeur_afni, level 1 (MICRO), type 0 (GENERAL)
Put quotes around (hopefully) every path, so spaces in paths are OK.
This is because of OneDrive. Grrrr.
06 Dec 2022, P Taylor, @SSwarper, level 1 (MICRO), type 0 (GENERAL)
Put quotes around (hopefully) every path, so spaces in paths are OK.
This is because of OneDrive. Grrrr.
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.
01 Dec 2022, P Taylor, align_epi_anat.py, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug: using -pre_matrix with -output_dir was broken.
Now internally use full path for pre_matrix (+bonus: check existence).
27 Nov 2022, P Taylor, @SSwarper, level 1 (MICRO), type 0 (GENERAL)
Update the help for integrating SSW with afni_proc.py (AP).
More readable, and simpler option usage
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, RC Reynolds, Makefile.macos_10.13_homebrew, level 1 (MICRO), type 5 (MODIFY)
rename Makefile.macOS_10.13_homebrew to Makefile.macos_10.13_homebrew
Done for consistency.
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
13 Oct 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
okay, fix 'final DF fraction' to be wrt uncensored TRs
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
06 Oct 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
replace aparc.a2009s+aseg.nii with aparc.a2009s+aseg_REN_all.nii.gz
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.
20 Sep 2022, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE)
make -timing_to_1D overlap error more clear
Thanks to the suffering of Y Takarae.
06 Sep 2022, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
remove specific commits from cmake/afni_project_dependencies.cmake
Build off of the current master.
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.
01 Sep 2022, P Taylor, 3dBrickStat, level 1 (MICRO), type 4 (BUG_FIX)
Fix bug: when using '-min' with '-positive' (or sim) and no mask.
Tended to return 0 (now fixed). Thanks for mentioning, Xiaowei!
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.
25 Aug 2022, P Taylor, 3ddelay, level 1 (MICRO), type 4 (BUG_FIX)
Make a tweak so that certain pathological cases don't scupper all others.
Thanks, D. Schwartz for pointing out this behavior.
23 Aug 2022, P Taylor, p2dsetstat, level 1 (MICRO), type 0 (GENERAL)
Expand stataux code range to 6.
Includes chi-square now.
23 Aug 2022, P Taylor, dsetstat2p, level 1 (MICRO), type 0 (GENERAL)
Expand stataux code range to 6.
Includes chi-square now.
23 Aug 2022, P Taylor, 3ddelay, level 1 (MICRO), type 4 (BUG_FIX)
Set correct dims being used from input dset in option_data struct.
Fixes report, and some internal instances (like micro/no change?).
19 Aug 2022, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
clean up some warnings in suma_utils.c (and retab and strip whitespace)
Thanks to markjens@github for noting them.
18 Aug 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 5 (MODIFY)
in basic script, do not cat any pre_ss_warn file, as output is now a dict
Thanks to PT for noting this.
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.
18 Aug 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 6 (ENHANCE)
In warns block check for 3dDeconvolve.err text file for warns.
If exists, most warns go to 'undecided' at the moment. Thanks, RCR!
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
17 Aug 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
if tlrc block and -regress_ROI*, require -volreg_tlrc_warp
Thanks to Mingbo on MB.
17 Aug 2022, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY)
allow rebuild of cjpeg/djpeg/libjpeg.a when any is missing
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.
12 Aug 2022, RC Reynolds, Makefile.INCLUDE, level 1 (MICRO), type 5 (MODIFY)
replace obsolete two-suffix rule with (.h) prerequisites
A target like .c.o or .c.$(SO) should not have extra prerequisites.
Use the more expanded form of '%.o : %.c ...' instead.
Also, fix an apparent unit var.
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
03 Aug 2022, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 4 (BUG_FIX)
3dDeconvolve currently misbehaves when there are no events for IM
Have the program terminate with an error, until the problem is resolved.
Thanks for T Clarkson for pointing out the problem.
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.
27 Jul 2022, P Taylor, dsetstat2p, level 1 (MICRO), type 0 (GENERAL)
Expand output precision and scale of calculability.
Program used to run into trouble for large stat (bc of bc); now better.
27 Jul 2022, P Taylor, apqc_make_tcsh.py, level 1 (MICRO), type 4 (BUG_FIX)
In mecho block when using m_tedana on Mac OS: fix copying tedana QC HTML.
Swap cp -> rsync, because Mac OS cp opts are diff than on Linux.
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.
22 Jul 2022, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
add linux_fedora_28_shared; we now distribute linux_fedora_35_shared
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.
24 Jun 2022, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 5 (MODIFY)
apply mask_epi_anat in help examples, rather than full_mask
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
13 Jun 2022, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
remove essentially duped final_epi_unif dset and uvar
07 Jun 2022, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 4 (BUG_FIX)
Fix how the AMASK_FOCUS_* keywords apply for '-box_focus_slices ..'.
They didn't work before, but now do/should/might/perhaps/pleeeez.
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.
18 May 2022, RC Reynolds, gen_ss_review_scripts.py, level 1 (MICRO), type 4 (BUG_FIX)
allow for pb00 dsets in standard space
Thanks to Erik (MB audachang) for noting it.
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.
10 May 2022, P Taylor, @djunct_overlap_check, level 1 (MICRO), type 2 (NEW_OPT)
Add -echo opt, and can propagate.
For debugging
10 May 2022, P Taylor, @djunct_edgy_align_check, level 1 (MICRO), type 2 (NEW_OPT)
Add -echo opt, and can propagate.
For debugging
10 May 2022, P Taylor, @SSwarper, level 1 (MICRO), type 2 (NEW_OPT)
Add -echo opt, and can propagate.
For debugging
10 May 2022, P Taylor, @SSwarper, level 1 (MICRO), type 0 (GENERAL)
Update/fix to mask resampling if present and if deobliqueing with 3dWarp.
Replace wsinc5 interp with NN interp---better for mask. Thanks, RCR!
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
03 May 2022, RC Reynolds, uber_subject.py, level 1 (MICRO), type 0 (GENERAL)
update to deal with minor changes to python modules
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.
auto-generated by afni_history on Apr 18 2024