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)  ----

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


25 Sep 2025, RC Reynolds, build_afni.py, level 1 (MICRO), type 6 (ENHANCE)
    add debug, a return at end of f_get_extras, and flush buffers

    Flush buffers any time we ask user to be patient.
    This helps with installs when scripts pipe (and so buffer) through tee.

25 Sep 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
    remove fix message regarding our code examples using 'tcsh'

    On the orders of PT.

25 Sep 2025, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
    OS_notes.macos_12_intel_b_user.tcsh : build_afni.py -fast_log_messages

    Do immediate message logging, in case of early user termination.


24 Sep 2025, DR Glen, afni, level 2 (MINOR), type 4 (BUG_FIX)
    Clusterize plugin wami command fix

    Temporary dataset deleted before getting name for whereami overlap omask.


23 Sep 2025, RC Reynolds, afni, level 1 (MICRO), type 5 (MODIFY)
    change default crosshair gap from 5 to 1

    This is controlled by AFNI_CROSSHAIRGAP.

23 Sep 2025, RC Reynolds, @SUMA_Make_Spec_FS, level 1 (MICRO), type 6 (ENHANCE)
    store FreeSurfer version in SUMA/version_fs.txt


18 Sep 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 6 (ENHANCE)
    report afnipy version

18 Sep 2025, DR Glen, afni, level 2 (MINOR), type 6 (ENHANCE)
    whereami functionality uses new Julich v3.1 brain atlases

    Julich v3.1 atlases for MNI 2009c and N27 spaces are available.
    Default atlas is now Julich_MNI2009c_v3.1 for Atlas Colors, Goto location.

18 Sep 2025, DR Glen, @MakeLabelTable, level 1 (MICRO), type 4 (BUG_FIX)
    @MakeLabelTable accepts leading 0 index values

    Accepts leading zeros but converts them to simple integers
    In order to avoid octal conversion errors in printf (008->error)


17 Sep 2025, RC Reynolds, afni, level 1 (MICRO), type 0 (GENERAL)
    add comment list of NAME2-enabled environment variables for grepping

    Done to appease the mighty D Glen.