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_months 6
---- 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
auto-generated by afni_history on Feb 24 2025