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)  ----

10 Apr 2026, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    update OS_notes.macos_12_*_a_admin_pt2.zsh to install R 4.5.2 (from 4.3.1)


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


03 Mar 2026, RC Reynolds, timing_tool.py, level 1 (MICRO), type 6 (ENHANCE)
    add help for evaluating TR-offset stats for non-binary TRs, like 1.3

03 Mar 2026, RC Reynolds, 3dDeconvolve, level 1 (MICRO), type 6 (ENHANCE)
    describe converting an HRF (long stimulus) to an IRF in the help


19 Feb 2026, RC Reynolds, make_random_timing.py, level 1 (MICRO), type 5 (MODIFY)
    add -tr_locked to g_style_opts_old

    Sorry about that, Catherine.

19 Feb 2026, RC Reynolds, SurfToSurf, level 1 (MICRO), type 6 (ENHANCE)
    add an example usage

    Inspired by P Molfese.


09 Feb 2026, RC Reynolds, timing_tool.py, level 1 (MICRO), type 4 (BUG_FIX)
    fix labels in -write_simple_tsv (they were truncated)


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


23 Jan 2026, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
    do not automatically include tcsh on check_list for init_user_dotfiles.py

    This prevents unneeded whining about apsearch in tcsh.
    Just let tcsh inherit variables when it is not the login shell.


22 Jan 2026, RC Reynolds, afni, level 1 (MICRO), type 4 (BUG_FIX)
    lose the C99 variable declaration, add new options to afni -help


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.

21 Jan 2026, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
    have AFNI_IMAGE_DATASETS default to NO

    Set it to YES to see jpg files in a directory (env var or .afnirc).
       e.g. afni -DAFNI_IMAGE_DATASETS=Y ~/abin
    Note that such files can be seen when directly passed on the command line.


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.


14 Jan 2026, RC Reynolds, install_bootcamp_data.tcsh, level 1 (MICRO), type 4 (BUG_FIX)
    handle -install_root as absolute path

    Thanks to P Taylor for noting this.


13 Jan 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    create enorm time series even if no volreg or censoring

    This is needed for APQC generation, so do it regardless.
    Thanks to Lauren_L on MB for the reminder.


09 Jan 2026, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    add -show_xmat_warnings after -show_cormat_warnings

    Warn about all-zero regressors or those with small maximum magnitudes.

09 Jan 2026, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 5 (MODIFY)
    if -prog_list given, have -build_source default to 'official'


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.


16 Dec 2025, RC Reynolds, 3dresample, level 1 (MICRO), type 5 (MODIFY)
    allow resampling to stay on current voxel grid, as much as possible

    Add -bound_type CENT/CENT_ORIG, add -up/downsample, -delta_scale.
    Done for PT.


15 Dec 2025, RC Reynolds, 3dcalc, level 1 (MICRO), type 5 (MODIFY)
    quiet some warnings

    If expr is 0 (or maybe 1), do not warn about all zeros or unused var.


05 Dec 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
    warn if the 'phia' R library has version 0.3.1


04 Dec 2025, RC Reynolds, plug_3dsvm, level 1 (MICRO), type 5 (MODIFY)
    cast function pointers to expected types in plug_3dsvm.c


18 Nov 2025, RC Reynolds, suma, level 1 (MICRO), type 4 (BUG_FIX)
    fix volume ray-trace voxel selection thresholding

    Thanks to Z Saad for bringing up the issue and cause :
       https://discuss.afni.nimh.nih.gov/t/voxel-selection-in-suma/9206