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 1
---- log of AFNI updates (most recent first) ----
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.
auto-generated by afni_history on Oct 31 2024