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)  ----

09 Oct 2026, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add and reorder rest examples under demo 2

    Add examples demo 2a: basic rest, 2b: ROI analysis, 2c: physio.
    Rename previous examples demo 2a and 2b to demo 2e and 2d.


06 Oct 2026, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add examples of use with fMRIPrep outputs - AP demo 3a,b,c


02 Oct 2026, RC Reynolds, Makefile.linux_ubuntu_26_ARM, level 2 (MINOR), type 2 (NEW_OPT)
    add Makefile.linux_ubuntu_26_ARM, a dupe of 24_ARM but SYSTEM_NAME


01 Oct 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
    allow for FMRIPREP_MOT* 1D column selectors

    These selectors will be expanded into fmriprep confound column sets.
      FMRIPREP_MOT          : rot_z,rot_x,rot_y,trans_z,trans_x,trans_y
      FMRIPREP_MOT_P2       : MOT, each appended with '_power2'
      FMRIPREP_MOT_DER      : MOT, each appended with '_derivative1'
      FMRIPREP_MOT_DER_P2   : MOT_DER, each appended with '_power2'


28 Sep 2026, RC Reynolds, src_notes, level 2 (MINOR), type 6 (ENHANCE)
    add src_notes/notes_afni_proc.txt - an overview of afni_proc.py


24 Sep 2026, RC Reynolds, @compute_OC_weights, level 1 (MICRO), type 6 (ENHANCE)
    allow for space in execution directory, and other minor updates


21 Sep 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 0 (GENERAL)
    minor cleanup - fix find_block, more apply_uopt_to_block


04 Sep 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 4 (BUG_FIX)
    if results dir already exists, properly report any -out_dir

    Thanks to S Francis for noting the problem.


02 Sep 2026, RC Reynolds, afni, level 2 (MINOR), type 5 (MODIFY)
    default change: AFNI_SKIP_TCSV_SCAN defaults to YES

    Now a recursive (maxdepth 4) search for CSV/TSV files will not happen
    by default.  It requires 'afni -yestcsv' or AFNI_SKIP_TCSV_SCAN=NO.


25 Aug 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
    no longer pass all_runs to @radial_correlate

25 Aug 2026, RC Reynolds, @radial_correlate, level 1 (MICRO), type 2 (NEW_OPT)
    add yes/no option -do_detrend

    By default, do not apply useless detrending to an errts dset.
    But if -do_detrend is given, apply as specified.


24 Aug 2026, RC Reynolds, suma, level 3 (MAJOR), type 6 (ENHANCE)
    (mostly from PL) update and merge in changes for BBox

24 Aug 2026, PD Lauren, suma, level 3 (MAJOR), type 6 (ENHANCE)
    Add Box feature (paired with Alpha) to match that of afni.

    Now 'A' (alpha) and 'B' (box) are similar to afni, with the new Box
    feature used to outline thresholded/clustered voxels (though Alpha does
    not currently work with clustering).


11 Jun 2026, RC Reynolds, 3dresample, level 1 (MICRO), type 6 (ENHANCE)
    add specific alloc check for signed int overflow

    Add more clarity to the life of C Walsh.


02 Jun 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 4 (BUG_FIX)
    fix setting tr - forgot to check in the original update for it

    Change original lib_afni1D:show_tpattern(), now require tr to be passed
    if one wants to override the class default of 1.


26 May 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 6 (ENHANCE)
    allow for new slice timing patterns, alt+z_D and alt-z_D

    Like alt+z, but generalized with a step of D slices, rather than just 2.
    Note that alt+z == alt+z_2.  There may be confusion with alt+z2, which
    is different.  Life is hard.
    The same relationships hold between alt-z_D and alt-z.
    Inspired by new data from D Handwerker.


18 May 2026, RC Reynolds, 3dCM, level 1 (MICRO), type 4 (BUG_FIX)
    if writing resample dset, preserve dirname

    Thanks to X Davis for noting the problem.


13 May 2026, RC Reynolds, 3dmask_tool, level 1 (MICRO), type 6 (ENHANCE)
    small improvement of info messages


12 May 2026, RC Reynolds, afni, level 3 (MAJOR), type 4 (BUG_FIX)
    macos 26.5+ now defaults to DO_AFNI_X11_REDRAW = NO

    The issue requiring redraw/forceExpose/Remanage events has been
    has been fixed by Apple as of macos 26.5.


30 Apr 2026, RC Reynolds, afni, level 1 (MICRO), type 6 (ENHANCE)
    add afni help details for DO_AFNI_X11_REDRAW and AFNI_X11_REDRAW_VERB


24 Apr 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    if tedana masking, suggest -blur_in_mask yes


21 Apr 2026, RC Reynolds, model_conv_PRF, level 1 (MICRO), type 6 (ENHANCE)
    be more descriptive of x and y, mapping stimulus orientation to results

21 Apr 2026, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
    show data dir history from the left, to include date


17 Apr 2026, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 6 (ENHANCE)
    add a help section, 'general rules for stimulus timing files'