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)  ----

04 Nov 2026, RC Reynolds, 3dmerge, level 2 (MINOR), type 4 (BUG_FIX)
    fix float initialization

    Short to float was not initialized at [0].  Also, blurring was not quite
    symmetric at volume edges.  A full edge mirror has now been applied for
    large volumes (>512), as it was for smaller ones.
    Thanks to Y Miyawaki for pointing out the [0] initialization.


03 Nov 2026, RC Reynolds, ap_run_simple_rest_me.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
    add -vline_num_pc

03 Nov 2026, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
    add -vline_num_pc

03 Nov 2026, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -find_var_line_npc, apply -find_var_line_opts


29 Oct 2026, RC Reynolds, afni_open, level 2 (MINOR), type 6 (ENHANCE)
    have afni_open -e respect the common EDITOR or VISUAL env vars

    Also, if vi, vim or nano, run in the foreground.
    We might want to add other editors to check for foreground execution.


27 Oct 2026, RC Reynolds, gen_ss_review_table.py, level 2 (MINOR), type 6 (ENHANCE)
    add example using APQC out.ss_review.*.json files


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