AFNI HISTORY

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_months 6 

  ----  log of AFNI updates (most recent first)  ----

13 Apr 2025, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
    quiet some compile warnings


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.

12 Apr 2025, RC Reynolds, get_afni_model_PRF_DN, level 1 (MICRO), type 1 (NEW_PROG)
    interface to compute model curve from parameters


08 Apr 2025, RC Reynolds, afni_general, level 1 (MICRO), type 5 (MODIFY)
    deal with homebrew updating cmake to 4.0.0 just after AFNI_25.0.13

    The cmake version was changed from 3.31.6 to 4.0.0, leading to a
    few needed updates.


04 Apr 2025, RC Reynolds, 3dTshift, level 1 (MICRO), type 5 (MODIFY)
    modify the -help to show slice timing in units of seconds

    Seconds are more common now.  Mention connection with dataset TR units.


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.


02 Apr 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    parse and pass any opts_ts -tpattern @FILE pattern to review_basic

    Thanks to colmconn on MB for pointing it out.


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

27 Feb 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
    add get_macos_mdls_val() for a deeper check on the XQuartz version


26 Feb 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
    note if 'afni' is owned by root or not user


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

04 Feb 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
    add build_afni.py to the list of AFNI programs to check


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

17 Nov 2024, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
    use xcode 15.1 in .circleci/config.yml

    Version 14.2 was too old (macos 12), and 15.3 has proto issues to fix.


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.