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) ----
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
25 Sep 2025, RC Reynolds, build_afni.py, level 1 (MICRO), type 6 (ENHANCE)
add debug, a return at end of f_get_extras, and flush buffers
Flush buffers any time we ask user to be patient.
This helps with installs when scripts pipe (and so buffer) through tee.
25 Sep 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
remove fix message regarding our code examples using 'tcsh'
On the orders of PT.
25 Sep 2025, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
OS_notes.macos_12_intel_b_user.tcsh : build_afni.py -fast_log_messages
Do immediate message logging, in case of early user termination.
24 Sep 2025, DR Glen, afni, level 2 (MINOR), type 4 (BUG_FIX)
Clusterize plugin wami command fix
Temporary dataset deleted before getting name for whereami overlap omask.
23 Sep 2025, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
change default crosshair gap from 5 to 1
This is controlled by AFNI_CROSSHAIRGAP.
23 Sep 2025, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 6 (ENHANCE)
store FreeSurfer version in SUMA/version_fs.txt
auto-generated by afni_history on Sep 19 2026