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 2026, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -post_elist_merge, to finally merge one condition into another
Added for C Walsh.
18 Oct 2026, RC Reynolds, install_bootcamp_data.tcsh, level 1 (MICRO), type 6 (ENHANCE)
when not downloading, allow install from above afni_boot_packages
16 Oct 2026, RC Reynolds, afni_open, level 2 (MINOR), type 6 (ENHANCE)
also search pub/dist/edu/data/sample; make repeated tries more clear
09 Oct 2026, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add and reorder rest examples under demo 2
Add examples demo 2a: basic rest, 2b: ROI analysis, 2c: physio.
Rename previous examples demo 2a and 2b to demo 2e and 2d.
06 Oct 2026, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add examples of use with fMRIPrep outputs - AP demo 3a,b,c
02 Oct 2026, RC Reynolds, Makefile.linux_ubuntu_26_ARM, level 2 (MINOR), type 2 (NEW_OPT)
add Makefile.linux_ubuntu_26_ARM, a dupe of 24_ARM but SYSTEM_NAME
01 Oct 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
allow for FMRIPREP_MOT* 1D column selectors
These selectors will be expanded into fmriprep confound column sets.
FMRIPREP_MOT : rot_z,rot_x,rot_y,trans_z,trans_x,trans_y
FMRIPREP_MOT_P2 : MOT, each appended with '_power2'
FMRIPREP_MOT_DER : MOT, each appended with '_derivative1'
FMRIPREP_MOT_DER_P2 : MOT_DER, each appended with '_power2'
28 Sep 2026, RC Reynolds, src_notes, level 2 (MINOR), type 6 (ENHANCE)
add src_notes/notes_afni_proc.txt - an overview of afni_proc.py
24 Sep 2026, RC Reynolds, @compute_OC_weights, level 1 (MICRO), type 6 (ENHANCE)
allow for space in execution directory, and other minor updates
21 Sep 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
minor cleanup - fix find_block, more apply_uopt_to_block
04 Sep 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
if results dir already exists, properly report any -out_dir
Thanks to S Francis for noting the problem.
02 Sep 2026, RC Reynolds, afni, level 2 (MINOR), type 5 (MODIFY)
default change: AFNI_SKIP_TCSV_SCAN defaults to YES
Now a recursive (maxdepth 4) search for CSV/TSV files will not happen
by default. It requires 'afni -yestcsv' or AFNI_SKIP_TCSV_SCAN=NO.
25 Aug 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
no longer pass all_runs to @radial_correlate
25 Aug 2026, RC Reynolds, @radial_correlate, level 1 (MICRO), type 2 (NEW_OPT)
add yes/no option -do_detrend
By default, do not apply useless detrending to an errts dset.
But if -do_detrend is given, apply as specified.
24 Aug 2026, RC Reynolds, suma, level 3 (MAJOR), type 6 (ENHANCE)
(mostly from PL) update and merge in changes for BBox
24 Aug 2026, PD Lauren, suma, level 3 (MAJOR), type 6 (ENHANCE)
Add Box feature (paired with Alpha) to match that of afni.
Now 'A' (alpha) and 'B' (box) are similar to afni, with the new Box
feature used to outline thresholded/clustered voxels (though Alpha does
not currently work with clustering).
11 Jun 2026, RC Reynolds, 3dresample, level 1 (MICRO), type 6 (ENHANCE)
add specific alloc check for signed int overflow
Add more clarity to the life of C Walsh.
02 Jun 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
fix setting tr - forgot to check in the original update for it
Change original lib_afni1D:show_tpattern(), now require tr to be passed
if one wants to override the class default of 1.
26 May 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
allow for new slice timing patterns, alt+z_D and alt-z_D
Like alt+z, but generalized with a step of D slices, rather than just 2.
Note that alt+z == alt+z_2. There may be confusion with alt+z2, which
is different. Life is hard.
The same relationships hold between alt-z_D and alt-z.
Inspired by new data from D Handwerker.
18 May 2026, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
if writing resample dset, preserve dirname
Thanks to X Davis for noting the problem.
13 May 2026, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 6 (ENHANCE)
small improvement of info messages
12 May 2026, RC Reynolds, afni, level 3 (MAJOR), type 4 (BUG_FIX)
macos 26.5+ now defaults to DO_AFNI_X11_REDRAW = NO
The issue requiring redraw/forceExpose/Remanage events has been
has been fixed by Apple as of macos 26.5.
30 Apr 2026, RC Reynolds, afni, level 1 (MICRO), type 6 (ENHANCE)
add afni help details for DO_AFNI_X11_REDRAW and AFNI_X11_REDRAW_VERB
24 Apr 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
if tedana masking, suggest -blur_in_mask yes
21 Apr 2026, RC Reynolds, model_conv_PRF, level 1 (MICRO), type 6 (ENHANCE)
be more descriptive of x and y, mapping stimulus orientation to results
21 Apr 2026, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
show data dir history from the left, to include date
17 Apr 2026, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 6 (ENHANCE)
add a help section, 'general rules for stimulus timing files'
10 Apr 2026, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
update OS_notes.macos_12_*_a_admin_pt2.zsh to install R 4.5.2 (from 4.3.1)
03 Apr 2026, RC Reynolds, @diff.tree, level 2 (MINOR), type 6 (ENHANCE)
make more space-friendly, adding quote and :q for most variable access
30 Mar 2026, RC Reynolds, suma, level 2 (MINOR), type 4 (BUG_FIX)
apply D Glen macos 26 X11 fixes on the suma side
27 Mar 2026, RC Reynolds, suma, level 2 (MINOR), type 4 (BUG_FIX)
fix problems causing crashes when using SUMA_SameSurfCont=NO
18 Mar 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -censor_to_spike_regs
Use this option to convert a 3dDeconvolve-style censor file
to an equivalent multi-column spike regressor file.
09 Mar 2026, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
on macos, check CPU type for gcc vs that of system
03 Mar 2026, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE)
add help for evaluating TR-offset stats for non-binary TRs, like 1.3
03 Mar 2026, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 6 (ENHANCE)
describe converting an HRF (long stimulus) to an IRF in the help
19 Feb 2026, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
add -tr_locked to g_style_opts_old
Sorry about that, Catherine.
19 Feb 2026, RC Reynolds, SurfToSurf, level 1 (MICRO), type 6 (ENHANCE)
add an example usage
Inspired by P Molfese.
09 Feb 2026, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
fix labels in -write_simple_tsv (they were truncated)
30 Jan 2026, DR Glen, afni, level 2 (MINOR), type 4 (BUG_FIX)
Overlay toggle fix
Overlay would not turn off properly with overlay 'o' key or Overlay button
23 Jan 2026, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
do not automatically include tcsh on check_list for init_user_dotfiles.py
This prevents unneeded whining about apsearch in tcsh.
Just let tcsh inherit variables when it is not the login shell.
22 Jan 2026, RC Reynolds, afni, level 1 (MICRO), type 4 (BUG_FIX)
lose the C99 variable declaration, add new options to afni -help
21 Jan 2026, RC Reynolds, afni, level 2 (MINOR), type 5 (MODIFY)
can specify whether to redraw, even on non-macos26
Have new options -x_needsX11Redraw() : do we redraw on resize?
-x_have_MACOS_FORCE_EXPOSE : is the compile flag set?
Use Y/N env var AFNI_DO_X11_REDRAW to force redrawing. Else, default
is still based on macos 26 and compile flag.
21 Jan 2026, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
have AFNI_IMAGE_DATASETS default to NO
Set it to YES to see jpg files in a directory (env var or .afnirc).
e.g. afni -DAFNI_IMAGE_DATASETS=Y ~/abin
Note that such files can be seen when directly passed on the command line.
20 Jan 2026, RC Reynolds, afni, level 3 (MAJOR), type 4 (BUG_FIX)
on macos 26, fully redraw any resized windows
The major updates were from RW Cox.
If using macos 26, resize events will have top-level windows call
XClearArea() and XSync(), and recursively on all children.
RW Cox rewrote AFNI graphs to continue drawing into fd_pxWind, but to
then copy this into the windows, rather than just having it as the
background.
Applying these 2 changes requires building with MACOS_FORCE_EXPOSE set,
currently done for both official mac systems.
RW Cox also added FIX_TOPFORM_HEIGHT to control window sizing in Linux.
These updates were also done with D Glen, who is now working on suma.
14 Jan 2026, RC Reynolds, install_bootcamp_data.tcsh, level 1 (MICRO), type 4 (BUG_FIX)
handle -install_root as absolute path
Thanks to P Taylor for noting this.
13 Jan 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
create enorm time series even if no volreg or censoring
This is needed for APQC generation, so do it regardless.
Thanks to Lauren_L on MB for the reminder.
09 Jan 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
add -show_xmat_warnings after -show_cormat_warnings
Warn about all-zero regressors or those with small maximum magnitudes.
09 Jan 2026, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
if -prog_list given, have -build_source default to 'official'
08 Jan 2026, RC Reynolds, install_bootcamp_data.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
new program to install the AFNI bootcamp data
Download and install all packages in the checksum file.
07 Jan 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_xmat_warnings
Warn on all-zero regressors or ones with small magnitudes.
16 Dec 2025, RC Reynolds, 3dresample, level 1 (MICRO), type 5 (MODIFY)
allow resampling to stay on current voxel grid, as much as possible
Add -bound_type CENT/CENT_ORIG, add -up/downsample, -delta_scale.
Done for PT.
15 Dec 2025, RC Reynolds, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
quiet some warnings
If expr is 0 (or maybe 1), do not warn about all zeros or unused var.
08 Dec 2025, DR Glen, asymm_report.csh, level 2 (MINOR), type 2 (NEW_OPT)
asymm_report.csh - surface patch asymmetry
Adding surface patch comparison to isosurface and volumes
05 Dec 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
warn if the 'phia' R library has version 0.3.1
04 Dec 2025, RC Reynolds, plug_3dsvm, level 1 (MICRO), type 5 (MODIFY)
cast function pointers to expected types in plug_3dsvm.c
18 Nov 2025, RC Reynolds, suma, level 1 (MICRO), type 4 (BUG_FIX)
fix volume ray-trace voxel selection thresholding
Thanks to Z Saad for bringing up the issue and cause :
https://discuss.afni.nimh.nih.gov/t/voxel-selection-in-suma/9206
auto-generated by afni_history on Oct 23 2026