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_months 6
---- 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.
auto-generated by afni_history on Apr 18 2024