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 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.


12 Sep 2025, DR Glen, afni, level 2 (MINOR), type 6 (ENHANCE)
    afni GUI can now sort datasets in chooser alphabetically

    Previously, sessions were sorted by anatomical, func, then NIFTI.
    Now the user has options to set alphabetic, reverse alphabetic,
    mri type (data type including NIFTI) or no re-sorting (original 
    mri type then NIFTI) using AFNI environment variables.


11 Sep 2025, RC Reynolds, afni_util.py, level 2 (MINOR), type 2 (NEW_OPT)
    add get_def_blur_from_dims() to report a hopefully useful blur size

    Set gmean = geometric mean(deltas), scale by 1.6 and take the ceiling,
    truncating to 4 significant bits.  So return:
    
        truncate_to_N_bits(gmean, bits=4, method='ceil', scale=1.6)

11 Sep 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    minor updates

    - suggest a new default blur (but still use 4.0), if none is given
    - suggest open_apqc.py instead of afni_open
    - allow verb only to show tracked files and create proc script
    - add example class do_21, to match that in AFNI_data7

11 Sep 2025, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
    OS_notes.macos_12_ARM_b_user.tcsh : also update .zshrc

    Some installs set PATH without updates, so update in each shell.


10 Sep 2025, RC Reynolds, ap_run_simple_rest_me.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
    add -blur_size; have default come from voxel sizes

    The default is now 1.1 times the geometric mean dim, ceiling rounded.

10 Sep 2025, RC Reynolds, ap_run_simple_rest.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
    add -blur_size; have default come from voxel sizes

    The default is now 1.6 times the geometric mean dim, ceiling rounded.

10 Sep 2025, RC Reynolds, test_ARMA_REML.tcsh, level 1 (MICRO), type 0 (GENERAL)
    extract the script from the end of 3dDeconvolve.c

    Having it in the .c file produce compile warnings.

10 Sep 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
    do not create a proc script on -show_tracked_files


09 Sep 2025, RC Reynolds, afni_util.py, level 1 (MICRO), type 2 (NEW_OPT)
    add 'ceil' option to truncate_to_N_bits; and removed repeated scaling

09 Sep 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
    look for AFNI_data7; better units evaluation on available disk space

09 Sep 2025, RC Reynolds, afni_system_check.py, level 1 (MICRO), type 5 (MODIFY)
    flask and flask_cors are now required

09 Sep 2025, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
    mac install: if brew is not initialized, do so

    Run 'brew shellenv' from OS_notes.macos_12_*_b_user.tcsh if need be.
    This if for JAMF, but can apply without.

09 Sep 2025, RC Reynolds, afni-general, level 1 (MICRO), type 4 (BUG_FIX)
    mac install: remove inappropriate backticks around 'which' command


08 Sep 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -regress_per_run_ortvec, to process physio_calc.py volbase regs

    The main outputs of physio_calc.py are *slibase.1D (for slice-based
    regressors) and *volbase.1D (for spatially global regressors).
    Keep using the -ricor options for *slibase.1D, but pass the *volbase.1D
    files using -regress_per_run_ortvec, with a label and one file per run.
    E.g.  -regress_per_run_ortvec Vphys resp_r1_volbase.1D resp_r2_volbase.1D


28 Aug 2025, RC Reynolds, gen_group_command.py, level 2 (MINOR), type 2 (NEW_OPT)
    try to detect BIDS; add option -sid_method

    This will also be incorporated in gen_ss_review_table.py.


19 Aug 2025, DR Glen, 3dXYZcat, level 1 (MICRO), type 4 (BUG_FIX)
    3dXYZcat generated extra empty volume in X direction


18 Aug 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -volreg_warp_master_box

    This is like -volreg_warp_master, but dxyz will come from EPI.
    If -volreg_warp_dxyz is given, _master is the same as _master_box.


15 Aug 2025, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -fast_log_commands and -fast_log_messages

15 Aug 2025, RC Reynolds, @compute_OC_weights, level 2 (MINOR), type 2 (NEW_OPT)
    add -prefix_combine, to combine the echoes using computed weights

    Added for P Molfese.


06 Aug 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add basic GTKYD (getting to know your data) and outlier check

    This will grow, including with user control.


29 Jul 2025, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    add option -force_write_type, to force output of simple, AM, DM or AM/DM


25 Jul 2025, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    gcc-15 : code updates under the SUMA tree

    This hopefully finalizes the June 12, 2025 update, including SUMA.


22 Jul 2025, RC Reynolds, @update.afni.binaries, level 1 (MICRO), type 2 (NEW_OPT)
    add option -binary_source, to supersede -build_afni and -overwrite_build