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_months 6 

  ----  log of AFNI updates (most recent first)  ----

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.


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.


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.


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


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


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.


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.


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.


17 Mar 2025, RC Reynolds, build_afni.py, level 2 (MINOR), type 4 (BUG_FIX)
    if -git_branch is non-master, do not apply default tag


12 Mar 2025, PD Lauren, suma, level 3 (MAJOR), type 5 (MODIFY)
    make |T|, 'sym I' and 'shw 0' apply to all surfaces


11 Mar 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    update examples class 3,5 per AD6; NL_warped_dsets requires e2a


07 Mar 2025, RC Reynolds, InstaTract, level 2 (MINOR), type 4 (BUG_FIX)
    add forgotten Wait_Till_Stream_Goes_Bad function (was using SUMA_)


06 Mar 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
    jpeg-6b/configure: save more details


27 Feb 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add options -show_merged_opts and -compare_merged_opts


24 Feb 2025, RC Reynolds, gen_ss_review_scripts.py, level 2 (MINOR), type 4 (BUG_FIX)
    no masking for max F on surface

24 Feb 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    avoid potential sub prefix when getting spec files

    Thanks to jmj0309 on MB for noting the issue.

24 Feb 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
    update Makefile.linux_ubuntu* (16,24,24_ARM) to distribute libgsl


11 Feb 2025, RC Reynolds, 3dROIstats, level 2 (MINOR), type 4 (BUG_FIX)
    fix nzvoxels and mode - had incorrectly applied float formatting


06 Feb 2025, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    allow -timing_to_1D with -multi_timing; add -timing_to_1D_method


04 Feb 2025, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
    allow direct updating of anyos_text* packages


03 Feb 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
    fix partial TAXIS_FLOATS attributes, created by 3drefit -Tslices

    Fill in missing zorg_sl, dz_sl, if they are zero and there are times.
    Fix in thd_dsetdblk.c for AFNI attributes in AFNI dsets.
    Fix in thd_initdblk.c for AFNI attributes in NIFTI dsets, though this
    change could have accomplished AFNI dsets, too.

03 Feb 2025, RC Reynolds, 3dROIstats, level 2 (MINOR), type 2 (NEW_OPT)
    add -float_format and -float_format_str, for floating point formatting

    Requested by P Molfese.


31 Jan 2025, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
    when setting slice times in edt_dsetitems.c, prevent dz_sl == 0

    This is required for (useful) display of timing in the afni GUI.
    Thanks to @martinsingua (AFNI MB) for noting the issue.

31 Jan 2025, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
    when writing NIFTI, allow for Siemens 2.5 ms timing resolution

    The 2.5 ms resolution as reported by the revered D Glen.

31 Jan 2025, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -show_slice_timing_resolution

    This is to help evaluate Siemens 2.5 ms slice time resolution.


29 Jan 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    suggest -combine_method OC_B over OC[_A] if only 2 echoes

29 Jan 2025, RC Reynolds, @extract_meica_ortvec, level 2 (MINOR), type 4 (BUG_FIX)
    allow for empty accept or reject lists

    Thanks to Avi (e0026902 on MB) for noting the problem.


28 Jan 2025, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -tlrc_affine_warped_dsets : a pre-computed affine std space xform

    Done for D Handwerker.