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 2 -past_years 1 

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

23 Oct 2026, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
    add option -post_elist_merge, to finally merge one condition into another

    Added for C Walsh.


16 Oct 2026, RC Reynolds, afni_open, level 2 (MINOR), type 6 (ENHANCE)
    also search pub/dist/edu/data/sample; make repeated tries more clear


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


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.


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).


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.


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.


03 Apr 2026, RC Reynolds, @diff.tree, level 2 (MINOR), type 6 (ENHANCE)
    make more space-friendly, adding quote and :q for most variable access


30 Mar 2026, RC Reynolds, suma, level 2 (MINOR), type 4 (BUG_FIX)
    apply D Glen macos 26 X11 fixes on the suma side


27 Mar 2026, RC Reynolds, suma, level 2 (MINOR), type 4 (BUG_FIX)
    fix problems causing crashes when using SUMA_SameSurfCont=NO


18 Mar 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -censor_to_spike_regs

    Use this option to convert a 3dDeconvolve-style censor file
    to an equivalent multi-column spike regressor file.


09 Mar 2026, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
    on macos, check CPU type for gcc vs that of system


30 Jan 2026, DR Glen, afni, level 2 (MINOR), type 4 (BUG_FIX)
    Overlay toggle fix

    Overlay would not turn off properly with overlay 'o' key or Overlay button


21 Jan 2026, RC Reynolds, afni, level 2 (MINOR), type 5 (MODIFY)
    can specify whether to redraw, even on non-macos26

    Have new options -x_needsX11Redraw() : do we redraw on resize?
                     -x_have_MACOS_FORCE_EXPOSE : is the compile flag set?
    Use Y/N env var AFNI_DO_X11_REDRAW to force redrawing.  Else, default
    is still based on macos 26 and compile flag.


20 Jan 2026, RC Reynolds, afni, level 3 (MAJOR), type 4 (BUG_FIX)
    on macos 26, fully redraw any resized windows

    The major updates were from RW Cox.
    If using macos 26, resize events will have top-level windows call
    XClearArea() and XSync(), and recursively on all children.
    RW Cox rewrote AFNI graphs to continue drawing into fd_pxWind, but to
    then copy this into the windows, rather than just having it as the
    background.
    Applying these 2 changes requires building with MACOS_FORCE_EXPOSE set,
    currently done for both official mac systems.
    RW Cox also added FIX_TOPFORM_HEIGHT to control window sizing in Linux.
    These updates were also done with D Glen, who is now working on suma.


08 Jan 2026, RC Reynolds, install_bootcamp_data.tcsh, level 3 (MAJOR), type 1 (NEW_PROG)
    new program to install the AFNI bootcamp data

    Download and install all packages in the checksum file.


07 Jan 2026, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -show_xmat_warnings

    Warn on all-zero regressors or ones with small magnitudes.


08 Dec 2025, DR Glen, asymm_report.csh, level 2 (MINOR), type 2 (NEW_OPT)
    asymm_report.csh - surface patch asymmetry

    Adding surface patch comparison to isosurface and volumes