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 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.
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
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
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
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
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.
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.
auto-generated by afni_history on Feb 24 2025