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)  ----

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


03 Jul 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
    fix test of atr_flt2 when setting TAXIS_FLOATS

    Thanks to C Rorden for noting the problem.


18 Jun 2025, RC Reynolds, build_afni.py, level 1 (MICRO), type 6 (ENHANCE)
    check that build_root is not at or under install dir


17 Jun 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    pass blur_size uvar to PT and APQC


12 Jun 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
    gcc-15 : code updates for building

    This is a partial update for building using gcc-15.
    The main change is that gcc-15 defaults to -std=gnu23 instead of
      -std=gnu17.  The main change between those standards being that
      empty function parameter lists are now taken as (void), so use of
      generic function pointers now needs casting to avoid errors of
      -Wincompatible-pointer-types.  Similarly, some K&R parameter styles
      must be updated to ANSI.
    This affects 135 files so far, and the SUMA tree is still to be done.


05 Jun 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
    add rt.22.py2py, to generally test client to server communication

    Added for S Fede.


02 Jun 2025, RC Reynolds, build_afni.py, level 1 (MICRO), type 6 (ENHANCE)
    display full make command before compiling

02 Jun 2025, RC Reynolds, afni-general, level 1 (MICRO), type 6 (ENHANCE)
    update OS_notes.macos_12_b_user.tcsh to skip homebrew gcc for now

    Use 'build_afni.py ... -cc_path /usr/bin/gcc' for now, until we
    resolve the issues with gcc-15.


21 May 2025, PD Lauren, suma, level 3 (MAJOR), type 5 (MODIFY)
    Made alpha variable opacity apply to all surfaces


16 May 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    add help for forgotten m_tedana_OC_tedort/OC_m_tedort combine methods


25 Apr 2025, RC Reynolds, 1d_tool.py, level 1 (MICRO), type 6 (ENHANCE)
    automatically replace n/a values with 0.0 when reading TSV

    And allow wildcard matching for column selectors.


24 Apr 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 5 (MODIFY)
    use updated find_variance_lines.tcsh (no -erode 2)

    The -ignore_edges method improves on the intention of -erode.


23 Apr 2025, RC Reynolds, afni.c, level 1 (MICRO), type 5 (MODIFY)
    add terminal handler to pass to XtAppSetErrorHandler

    This is needed to use __attribute__((noreturn)) for macos /usr/bin/gcc.
    Added for J Kadlec.


21 Apr 2025, RC Reynolds, find_variance_lines.tcsh, level 2 (MINOR), type 2 (NEW_OPT)
    add -ignore_edges, to help avoid reporting motion-based variance lines


13 Apr 2025, RC Reynolds, afni-general, level 1 (MICRO), type 5 (MODIFY)
    quiet some compile warnings


12 Apr 2025, RC Reynolds, model_conv_PRF_DN, level 2 (MINOR), type 1 (NEW_PROG)
    add Divisive Normalization population receptive field model

    Requested by E Merriam.

12 Apr 2025, RC Reynolds, get_afni_model_PRF_DN, level 1 (MICRO), type 1 (NEW_PROG)
    interface to compute model curve from parameters


08 Apr 2025, RC Reynolds, afni_general, level 1 (MICRO), type 5 (MODIFY)
    deal with homebrew updating cmake to 4.0.0 just after AFNI_25.0.13

    The cmake version was changed from 3.31.6 to 4.0.0, leading to a
    few needed updates.


04 Apr 2025, RC Reynolds, 3dTshift, level 1 (MICRO), type 5 (MODIFY)
    modify the -help to show slice timing in units of seconds

    Seconds are more common now.  Mention connection with dataset TR units.


03 Apr 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
    add rt.21.py2rr example, send mot and ROI aves 2 rr via python

    Demonstrate the basics of sending motion parameters and ROI averages
    to realtime_receiver.py.


02 Apr 2025, RC Reynolds, afni_proc.py, level 1 (MICRO), type 6 (ENHANCE)
    parse and pass any opts_ts -tpattern @FILE pattern to review_basic

    Thanks to colmconn on MB for pointing it out.


29 Mar 2025, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
    add -sort_method geme_rin back in

    This method is like geme_index, but uses RIN for the initial sort.
    Thanks to Shruti for reminding of its usefulness.


28 Mar 2025, RC Reynolds, APMULTI_Demo2_realtime, level 2 (MINOR), type 6 (ENHANCE)
    add rt.20.python example, data 2 afni -rt via python

    Demonstrate the basics of sending data to 'afni -rt'.


24 Mar 2025, RC Reynolds, Dimon, level 2 (MINOR), type 2 (NEW_OPT)
    add -sort_method echo_rin

    This works well if RIN repeats per volume and echo, and echo is set.
    geme_rin was temporarily removed, but that angered the mighty Shruti.


21 Mar 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add combine methods OC_m_tedort and m_tedana_OC_tedort

    These are additional methods using the MEICA group tedana.  They both
    extract the tedort regressors (reject, but with accept projected out),
    using OC data and passing the tedort regressors to the final regression.


20 Mar 2025, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    add option -select_cols_via_TSV_table

    This was intended for processing tedana output.  Given a TSV component
    file as -input, the new option allows one to select accepted or rejected
    components via the metrics.tsv table.