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) ---- 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
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.
07 Mar 2024, RC Reynolds, abids_tool.py, level 1 (MICRO), type 4 (BUG_FIX) use compare_py_ver_to_given() for comparison of python versions Also, removed a few similarly problematic float comparisons.
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 wanings 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.
23 Feb 2024, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE) sync crorden/dcm2niix_console with repo, version v1.0.20240202 Thanks to C Rorden for the update. 23 Feb 2024, RC Reynolds, @radial_correlate, level 1 (MICRO), type 6 (ENHANCE) fail if no corr dset (check, since script is not run with -e)
22 Feb 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE) check for conda env vars on make build failure 22 Feb 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) check for conda env vars 22 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) use more mask_epi_anat, and default: -regress_compute_tsnr_stats brain 1
21 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 2 (MINOR), type 5 (MODIFY) modify labels and prep for Q column
20 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 1 (MICRO), type 4 (BUG_FIX) forgot to actually print out the computed depth Thanks to P Taylor for noticing. 20 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) remove irritating -script and -out_dir opts, just use subject ID
15 Feb 2024, RC Reynolds, compute_ROI_stats.tcsh, level 3 (MAJOR), type 1 (NEW_PROG) compute per-ROI region statstics over a given dataset It is a little like 3dROIstats, but with needs specific to afni_proc.py. 15 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -regress_compute_tsnr_stats This is intended to be added to P Taylor's APQC HTML report. 15 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) remove 2 warnings No warn on dupe followers if grids are the same; no ACF warning.
14 Feb 2024, DR Glen, whereami, level 1 (MICRO), type 2 (NEW_OPT) whereami -index_to_label to show label for an index Labels can be from ordinary labeltabled ROI datasets or from atlas datasets
08 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) in radcor: pass mask after any data scaling or in regress block Scaled or errts data won't automask well. Also, block radcor once in the surface domain.
07 Feb 2024, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 6 (ENHANCE) add regress to -radial_correlate_blocks Also, handle new DEFAULT example names, and pass using underscores. 07 Feb 2024, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) allow underscores in example names, and convert to spaces
05 Feb 2024, RC Reynolds, @FindAfniDsetPath, level 2 (MINOR), type 5 (MODIFY) one change to allow spaces in dataset names Spaces in the paths to templates/atlases or the abin is currently not allowed. But we might slowly change that. 05 Feb 2024, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX) change GIFTI write from PREFIX to HEADNAME Previously, the output directories were not being used. Thanks to eriklee (AFNI MB) for noting the problem.
02 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) add -ROI_import (in prep for TSNR stats)
01 Feb 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT) -show_example_keywords, -show_pythonic_command; revamp examples
21 Jan 2024, RC Reynolds, file_tool, level 2 (MINOR), type 2 (NEW_OPT) add -wrap_text and -wrap_text_method for more clear command line use 21 Jan 2024, RC Reynolds, afni_util.py, level 2 (MINOR), type 5 (MODIFY) redo deep PT special
19 Jan 2024, RC Reynolds, afni_util.py, level 1 (MICRO), type 5 (MODIFY) have wrap_file_text() default to wrap=2 in nwrite_text_to_file()
18 Jan 2024, RC Reynolds, 3dZeropad, level 2 (MINOR), type 2 (NEW_OPT) add options -pad2odds, -pad2mult (pad to any positive multiple) Motivated by P Taylor.
11 Jan 2024, RC Reynolds, afni, level 2 (MINOR), type 4 (BUG_FIX) validate fim_now in AFNI_autorange_label If the underlay existed in both orig and tlrc view, switching to the view without an overlay would cause a crash. Thanks to msh23m (AFNI message board) for noting the problem.
02 Jan 2024, RC Reynolds, init_user_dotfiles.py, level 1 (MICRO), type 6 (ENHANCE) apply apsearch updates only if shell file applies to current or login 02 Jan 2024, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) warn on matplotlib version 3.1.2 for not being able to write JPEG
22 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX) get a new idcode whenever a new dataset name is assigned This deals with programs like 3dTsplit4D creating multiple datasets, as well as programs like afni reading many similarly named files Thanks for J Blujus for reminding of the issue.
21 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX) allow nim->nvox to exceed int32_t range with NIFTI-1 output Thanks to P Rais-Roldan for noting the discrepancy. 21 Dec 2023, RC Reynolds, afni-general, level 1 (MICRO), type 2 (NEW_OPT) add AFNI_NIFTI_WRITE_TYPE to override choice of NIFTI-1 or -2 output
08 Dec 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 4 (BUG_FIX) copy README files into build_src; use prev directory, not prefix Thanks to D Glen for noting the missing README files.
07 Dec 2023, RC Reynolds, @update.afni_binaries, level 2 (MINOR), type 2 (NEW_OPT) add -overwrite_build This option is now required to allow @uab to run and overwrite a local binary package that was created using build_afni.py.
04 Dec 2023, RC Reynolds, timing_tool.py, level 2 (MINOR), type 6 (ENHANCE) allow more n/a fields in tsv files
27 Nov 2023, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE) add some comments about build_afni.py
24 Nov 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) add -disp_ver_pylibs Show python library __version__ strings. Check for flask and flask_cors with -check_all.
20 Nov 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT) add 'rsync_preserve' backup_method; rsync now cleans abin after backup Prior to this, abin was allowed to accumulate files. That is no longer the default operation.
14 Nov 2023, RC Reynolds, 3dNLfim, level 2 (MINOR), type 4 (BUG_FIX) when creating non-bucket output, if float output, make all volumes float Thanks to V Dinh for noting the problem.
30 Oct 2023, RC Reynolds, Makefile.macos_13_ARM_clang, level 2 (MINOR), type 5 (MODIFY) (w/DG) use homebrew gcc-13, and downgrade -O2 to -O1 We have yet to resolve why /usr/bin/gcc led to a 3dSkullStrip crash. And brew gcc-13 led to a 3dvolreg crash, but that seems to be due to failed compiler optimizations. Using -O1 works.
12 Oct 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 5 (MODIFY) only require flat_namespace if 10.12_local or 10.7_local
10 Oct 2023, RC Reynolds, init_user_dotfiles.py, level 2 (MINOR), type 5 (MODIFY) allow -do_updates to override all updates from -test 10 Oct 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 5 (MODIFY) require -build_root; tail build errors; default to atlas updating
28 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) add option -disp_R_ver_for_lib 28 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) split OS_notes_macos_12 by CPU Now have : OS_notes.macos_12_{ARM,intel}_a_admin.zsh and : OS_notes.macos_12_{ARM,intel}_b_user.tcsh The b_user scripts still just run OS_notes.macos_12_b_user.tcsh.
26 Sep 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT) install NiiVue; add option -update_atlases, to download newest package
22 Sep 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) in examples, change MNI152_T1_2009c+tlrc to MNI152_2009_template.nii.gz
21 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) capture the platform of the R version
18 Sep 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 2 (NEW_OPT) add option -use_asc_path, to test using directory of afni_system_check.py
15 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) have all R wrapper scripts (scripts_for_r) return the status from R To match returning non-zero when loading R_io.so. 15 Sep 2023, RC Reynolds, init_user_dotfiles.py, level 1 (MICRO), type 6 (ENHANCE) in .zshrc, pass -i to compinit, to ignore insecure files Whines from compaudit: files not owned by root or user or with perm g+w. Done with D Glen.
13 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) create OS_notes.macos_12_b_user.tcsh to be an executable install script Have OS_notes.macos_12_x86_64_b_user.txt just execute the new script. Reluctantly done to appease D Glen (thanks). 13 Sep 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 4 (BUG_FIX) have 1d_tool.py -write_xstim create an empty file if empty matrix This got lost, but is needed for @ss_review_basic on rest data.
08 Sep 2023, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT) new operation: by default, back up and install the build results This is a change in behavior. Upon a successful build, default is now back up the ABIN and install new binaries and atlases. Add options -abin, -do_backup, -do_install, -backup_method.
07 Sep 2023, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX) change afni/build to afni_build in OS_notes.macos_12_x86_64_b_user.txt Thanks to spartaaa-git@github.com for pointing that out.
01 Sep 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add -show_slice_timing_gentle Also, use mean timing diff rather than median.
28 Aug 2023, RC Reynolds, test_afni_prog_help.tcsh, level 2 (MINOR), type 6 (ENHANCE) rename from test.afni.prog.help and moved to scripts_install This is now distributed for more general testing. 28 Aug 2023, RC Reynolds, build_afni.py, level 1 (MICRO), type 5 (MODIFY) apply renamed test_afni_prog_help.tcsh program
21 Aug 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) apply uncensored TRs via a text file rather than command line With a long encoded TR list, file names might exceed the allowable limit (currently about 5100 bytes), e.g. data+tlrc'[3,5..7,10..13,23]'. Instead, use the 1dcat functionality to get those volume indices from a text file. So if trs.txt contains 3 5 6 7 10 11 12 13 23, then one can read the volumes using data+tlrc'[1dcat trs.txt]'. Thanks to G Edwards and S Japee for diagnosing the issue.
17 Aug 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT) add option -slice_pattern_to_times Output timing given known to3d tpattern, nslices, multiband level, and TR. 17 Aug 2023, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE) rewrite -show_slice_timing_pattern Be more forgiving in timing when trying to detect a pattern.
16 Aug 2023, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE) sync crorden/dcm2niix_console with repo, version v1.0.20230411 Thanks to C Rorden for the update. 16 Aug 2023, RC Reynolds, dcm2niix_afni, level 1 (MICRO), type 6 (ENHANCE) turn off local signing in crorden/dcm2niix_console/makefile
08 Aug 2023, RC Reynolds, 3dLocalstat, level 2 (MINOR), type 4 (BUG_FIX) when creating bucket output, clear time dimension Thanks to Philip on MB for noting the problem.
27 Jul 2023, RC Reynolds, afni-general, level 2 (MINOR), type 1 (NEW_PROG) distribute niiview as niiview_afni.umd.js This is intended to be used via P Taylor's APQC HTML report. Requested by P Taylor.
24 Jul 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY) if -tlrc_NL_warped_dsets, require -tlrc_base Require user to verify which template was used to make warped dsets. Requested by D Glen.
21 Jul 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) fix help for -regress_make_corr_vols It WAS ave corr, but as of Jan 2020, it is corr of voxels vs ave. Thanks to D Glen for noting the discrepancy.
19 Jul 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 4 (BUG_FIX) fix use of min instead of minor Thanks to @dojoonyi for letting us know.
26 Jun 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) write NIFTI-2 if dimensions require it
22 Jun 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX) pass tlrc_base uvar as template Sorry, PT.
20 Jun 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE) under linux, check for shared dependencies of R_io.so
14 Jun 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY) default to -radial_correlate_blocks errts, if none given
08 Jun 2023, RC Reynolds, Makefile.INCLUDE, level 2 (MINOR), type 6 (ENHANCE) add build maker to AFNI_version.txt 08 Jun 2023, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY) turn off check for PyQt4
07 Jun 2023, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE) start looking for dependent libraries (under linux for now) Also, rearranged some of the output. Done at the behest of P Taylor.
02 Jun 2023, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX) fix -regress_errts_prefix for surface analysis It was missing $hemi to specify the hemisphere. Thanks to A Gilemore for bringing up the issue.
12 May 2023, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY) R-3.6.3.nn.pkg has been moved to cran-archive.r-project.org Thanks to Sally D for letting us know. 12 May 2023, RC Reynolds, Makefile.macos_13_ARM_clang, level 1 (MICRO), type 5 (MODIFY) comment out EXTRA_INSTALL_FILES Might vary, and is not needed for non-distribution system.
10 May 2023, RC Reynolds, Makefile.macos_12_x86_64, level 2 (MINOR), type 2 (NEW_OPT) add Makefile, updates, and OS_notes
05 May 2023, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE) distribute prog_list.txt (and _bin and _scripts) Later we will (modify) and distribute test.afni.prog.help, perhaps. 05 May 2023, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 4 (BUG_FIX) fix error cur_afni error if no AFNI is present This was failing to finish setting up dot files.
02 May 2023, RC Reynolds, RetroTS.py, level 1 (MICRO), type 5 (MODIFY) numpy.complex() is deprecated, use complex()
27 Apr 2023, RC Reynolds, Isosurface, level 2 (MINOR), type 4 (BUG_FIX) include updates for the 2002.08.12 MarchingCubes code base Thanks to C Rorden for providing an updated translation.
25 Apr 2023, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE) note possibly using the regress block in -radial_correlate_blocks This might be particularly useful with ANATICOR.
20 Apr 2023, RC Reynolds, NIFTI, level 2 (MINOR), type 6 (ENHANCE) sync with NIFTI-Imaging/nifti_clib
19 Apr 2023, RC Reynolds, APMULTI_Demo1_rest, level 2 (MINOR), type 6 (ENHANCE) add do/run_40* scripts These are in the apmulti_scripts repo.
14 Apr 2023, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE) add Makefile.linux_rocky_8 and OS_notes.linux_rocky_8.txt These should work on RHEL/CentOS/Rocky/Almalinux 8. This is now a new build package.
06 Apr 2023, P Taylor, afni_util.py, level 2 (MINOR), type 0 (GENERAL) Add new functions for shell_com logging (kind like history ). write_afni_com_log(), proc_log(), format_log_dict(). 06 Apr 2023, P Taylor, afni_base.py, level 2 (MINOR), type 0 (GENERAL) Add new attribute/methods for shell_com logging (kinda like history). save_log, add_to_log, shell_log, etc.
03 Apr 2023, RC Reynolds, @diff.tree, level 2 (MINOR), type 6 (ENHANCE) update @diff.tree, @diff.files: possibly switch to meld if no xxdiff Be automatic, rather than forcing one to use '-diff_prog meld'.

auto-generated by afni_history on Mar 24 2024