AFNI HISTORY
level 2 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 2 -past_years 1
---- log of AFNI updates (most recent first) ----
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.
18 Sep 2025, DR Glen, afni, level 2 (MINOR), type 6 (ENHANCE)
whereami functionality uses new Julich v3.1 brain atlases
Julich v3.1 atlases for MNI 2009c and N27 spaces are available.
Default atlas is now Julich_MNI2009c_v3.1 for Atlas Colors, Goto location.
12 Sep 2025, DR Glen, afni, level 2 (MINOR), type 6 (ENHANCE)
afni GUI can now sort datasets in chooser alphabetically
Previously, sessions were sorted by anatomical, func, then NIFTI.
Now the user has options to set alphabetic, reverse alphabetic,
mri type (data type including NIFTI) or no re-sorting (original
mri type then NIFTI) using AFNI environment variables.
11 Sep 2025, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add get_def_blur_from_dims() to report a hopefully useful blur size
Set gmean = geometric mean(deltas), scale by 1.6 and take the ceiling,
truncating to 4 significant bits. So return:
truncate_to_N_bits(gmean, bits=4, method='ceil', scale=1.6)
11 Sep 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
minor updates
- suggest a new default blur (but still use 4.0), if none is given
- suggest open_apqc.py instead of afni_open
- allow verb only to show tracked files and create proc script
- add example class do_21, to match that in AFNI_data7
10 Sep 2025, RC Reynolds, ap_run_simple_rest_me.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add -blur_size; have default come from voxel sizes
The default is now 1.1 times the geometric mean dim, ceiling rounded.
10 Sep 2025, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add -blur_size; have default come from voxel sizes
The default is now 1.6 times the geometric mean dim, ceiling rounded.
08 Sep 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -regress_per_run_ortvec, to process physio_calc.py volbase regs
The main outputs of physio_calc.py are *slibase.1D (for slice-based
regressors) and *volbase.1D (for spatially global regressors).
Keep using the -ricor options for *slibase.1D, but pass the *volbase.1D
files using -regress_per_run_ortvec, with a label and one file per run.
E.g. -regress_per_run_ortvec Vphys resp_r1_volbase.1D resp_r2_volbase.1D
28 Aug 2025, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
try to detect BIDS; add option -sid_method
This will also be incorporated in gen_ss_review_table.py.
18 Aug 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -volreg_warp_master_box
This is like -volreg_warp_master, but dxyz will come from EPI.
If -volreg_warp_dxyz is given, _master is the same as _master_box.
15 Aug 2025, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
add -fast_log_commands and -fast_log_messages
15 Aug 2025, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT)
add -prefix_combine, to combine the echoes using computed weights
Added for P Molfese.
06 Aug 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add basic GTKYD (getting to know your data) and outlier check
This will grow, including with user control.
29 Jul 2025, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -force_write_type, to force output of simple, AM, DM or AM/DM
25 Jul 2025, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
gcc-15 : code updates under the SUMA tree
This hopefully finalizes the June 12, 2025 update, including SUMA.
03 Jul 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix test of atr_flt2 when setting TAXIS_FLOATS
Thanks to C Rorden for noting the problem.
12 Jun 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
gcc-15 : code updates for building
This is a partial update for building using gcc-15.
The main change is that gcc-15 defaults to -std=gnu23 instead of
-std=gnu17. The main change between those standards being that
empty function parameter lists are now taken as (void), so use of
generic function pointers now needs casting to avoid errors of
-Wincompatible-pointer-types. Similarly, some K&R parameter styles
must be updated to ANSI.
This affects 135 files so far, and the SUMA tree is still to be done.
05 Jun 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
add rt.22.py2py, to generally test client to server communication
Added for S Fede.
21 May 2025, PD Lauren, suma, level 3 (MAJOR), type 5 (MODIFY)
Made alpha variable opacity apply to all surfaces
21 Apr 2025, RC Reynolds, find_variance_lines.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add -ignore_edges, to help avoid reporting motion-based variance lines
12 Apr 2025, RC Reynolds, model_conv_PRF_DN, level 2 (MINOR), type 1 (NEW_PROG)
add Divisive Normalization population receptive field model
Requested by E Merriam.
03 Apr 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
add rt.21.py2rr example, send mot and ROI aves 2 rr via python
Demonstrate the basics of sending motion parameters and ROI averages
to realtime_receiver.py.
29 Mar 2025, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
add -sort_method geme_rin back in
This method is like geme_index, but uses RIN for the initial sort.
Thanks to Shruti for reminding of its usefulness.
28 Mar 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
add rt.20.python example, data 2 afni -rt via python
Demonstrate the basics of sending data to 'afni -rt'.
24 Mar 2025, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
add -sort_method echo_rin
This works well if RIN repeats per volume and echo, and echo is set.
geme_rin was temporarily removed, but that angered the mighty Shruti.
21 Mar 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add combine methods OC_m_tedort and m_tedana_OC_tedort
These are additional methods using the MEICA group tedana. They both
extract the tedort regressors (reject, but with accept projected out),
using OC data and passing the tedort regressors to the final regression.
20 Mar 2025, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add option -select_cols_via_TSV_table
This was intended for processing tedana output. Given a TSV component
file as -input, the new option allows one to select accepted or rejected
components via the metrics.tsv table.
17 Mar 2025, RC Reynolds, build_afni.py, level 2 (MINOR), type 4 (BUG_FIX)
if -git_branch is non-master, do not apply default tag
12 Mar 2025, PD Lauren, suma, level 3 (MAJOR), type 5 (MODIFY)
make |T|, 'sym I' and 'shw 0' apply to all surfaces
11 Mar 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
update examples class 3,5 per AD6; NL_warped_dsets requires e2a
07 Mar 2025, RC Reynolds, InstaTract, level 2 (MINOR), type 4 (BUG_FIX)
add forgotten Wait_Till_Stream_Goes_Bad function (was using SUMA_)
06 Mar 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
jpeg-6b/configure: save more details
27 Feb 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
add options -show_merged_opts and -compare_merged_opts
24 Feb 2025, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
no masking for max F on surface
24 Feb 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
avoid potential sub prefix when getting spec files
Thanks to jmj0309 on MB for noting the issue.
24 Feb 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
update Makefile.linux_ubuntu* (16,24,24_ARM) to distribute libgsl
11 Feb 2025, RC Reynolds, 3dROIstats, level 2 (MINOR), type 4 (BUG_FIX)
fix nzvoxels and mode - had incorrectly applied float formatting
06 Feb 2025, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
allow -timing_to_1D with -multi_timing; add -timing_to_1D_method
04 Feb 2025, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
allow direct updating of anyos_text* packages
03 Feb 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
fix partial TAXIS_FLOATS attributes, created by 3drefit -Tslices
Fill in missing zorg_sl, dz_sl, if they are zero and there are times.
Fix in thd_dsetdblk.c for AFNI attributes in AFNI dsets.
Fix in thd_initdblk.c for AFNI attributes in NIFTI dsets, though this
change could have accomplished AFNI dsets, too.
03 Feb 2025, RC Reynolds, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
add -float_format and -float_format_str, for floating point formatting
Requested by P Molfese.
31 Jan 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
when setting slice times in edt_dsetitems.c, prevent dz_sl == 0
This is required for (useful) display of timing in the afni GUI.
Thanks to @martinsingua (AFNI MB) for noting the issue.
31 Jan 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
when writing NIFTI, allow for Siemens 2.5 ms timing resolution
The 2.5 ms resolution as reported by the revered D Glen.
31 Jan 2025, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_slice_timing_resolution
This is to help evaluate Siemens 2.5 ms slice time resolution.
29 Jan 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
suggest -combine_method OC_B over OC[_A] if only 2 echoes
29 Jan 2025, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 4 (BUG_FIX)
allow for empty accept or reject lists
Thanks to Avi (e0026902 on MB) for noting the problem.
28 Jan 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
add -tlrc_affine_warped_dsets : a pre-computed affine std space xform
Done for D Handwerker.
27 Jan 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
fix -compare_opts display of fewer/more options applied
27 Jan 2025, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
w/DRG: invoke all tcsh scripts with env tcsh, rather than tcsh directly
To allow for other tcsh versions in the PATH, remove the direct path to
tcsh in the top execution lines, using env tcsh instead. This is mostly
to work around tcsh version 6.22.03 which breaks :h with an absolute
path.
This change applies to 180 files. Most changes are just to the top
execution line, but any 'tcsh -e' usage means additional checking for
$status failures.
There might still be some script generation changes to make, such as
to afni_procp.py.
23 Jan 2025, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
more checks for mac gcc, test rPkgsInstall
13 Jan 2025, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
updates for OS version, gcc and CLT SDK
08 Jan 2025, RC Reynolds, find_variance_lines.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
add -thresh and -stdev_power; init min_cvox to 7
06 Jan 2025, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT)
warn user of ARM mac using macos_10.12_local
17 Dec 2024, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
add a simple convolve function
17 Dec 2024, RC Reynolds, Makefile.linux_ubuntu_24_ARM, level 2 (MINOR), type 2 (NEW_OPT)
duplicate the 24_64 Makefile but with the ARM system name
10 Dec 2024, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_modulator_stats option, showing min,mean,max,stdev stats
06 Dec 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
subtract 1 from ricor QC vrat, for more a useful display
Previously output ratio of orig/ricor variances to view improvement.
Subtract 1 for better visualization, since the orig ratio must be > 1,
leaving the image as a more direct 'fractional improvement', say.
Or equivalently, call it (orig-ricor)/ricor.
17 Nov 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
add -make_flags option
11 Nov 2024, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
add -show_tr_offset_stats
This enhances -show_tr_stats, and might replace it.
A start to what was requested by Gang.
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.
auto-generated by afni_history on Sep 29 2025