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)  ----

23 Oct 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    add -volreg_no_volreg

    Replace the 3dvolreg alignment transformation with the identity.
    The B Feige option.


10 Oct 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    mask intersect inputs did not have views

    Thanks to martinsingua on the MB for pointing out the problem.


04 Oct 2024, RC Reynolds, gen_group_command.py, level 3 (MAJOR), type 2 (NEW_OPT)
    add -datatable 'command', to generate table for R stats programs

    Use gen_group_command.py -command datatable to generate datatable files
    for -dataTable options, for programs like 3dMVM, 3dLME, etc.


24 Sep 2024, RC Reynolds, 3dTsplit4D, level 2 (MINOR), type 4 (BUG_FIX)
    fix confusion over auto-gzip BRIK name


19 Sep 2024, RC Reynolds, @update.afni.binaries, level 2 (MINOR), type 6 (ENHANCE)
    allow use of build_afni.py for updating the current package

    If build_afni.py was used to create the current package, then @uab
    will also use it for updating (rather than downloading an official
    package.  One can also specify to use it via -build_afni.


16 Sep 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
    if which Xvfb fails, check for its existence on disk

    Also, include .login and report fewer homebrew link suggestions.

16 Sep 2024, RC Reynolds, afni-general, level 2 (MINOR), type 6 (ENHANCE)
    apply LOCAL_CC_PATH in Makefile.macos_13_ARM and Makefile.macos_12_x86_64


13 Sep 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    in eispack C files, include math.h before f2c.h

    This should generally have no effect, since the local f2c.h
    includes math.h.  However, if one is using cmake and the system
    f2c for linking (rather than using afni/src/f2c), then the f2c.h
    included with the eispack files will not have math.h.
    So locally include math.h, just to be sure.


12 Sep 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE)
    add option -cc_path

    Allow one to pass an alternate compiler if the relevant Makefile
    uses LOCAL_CC_PATH.  If this option is not used and the default
    compiler does not exist, try to find the most recent similar version.


11 Sep 2024, P Taylor, gtkyd_check, level 2 (MINOR), type 7 (REMOVE)
    Remove the *tcsh script* version of gtkyd_check.

    This has now been superseded by a Python version of same name.


10 Sep 2024, P Taylor, gtkyd_check, level 3 (MAJOR), type 1 (NEW_PROG)
    A *Python* version of previously-written tcsh script of same name.

    Much faster way of checking/tabulating a glob of datasets for properties.


04 Sep 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 5 (MODIFY)
    use uname -m for CPU, instead of platform.processor()

04 Sep 2024, RC Reynolds, OS_notes.macos_12_b_user.tcsh, level 2 (MINOR), type 6 (ENHANCE)
    allow the script to be re-run with no effect


30 Aug 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    many updates to help examples; separate paths in compare_opts

    - make example option order more consistent
    - add examples: publish 3e ... 3j
    - exclude 'noshow' examples from default help (currently 3e,f,g,h,j)
    - separate differing paths in -compare_opts


05 Aug 2024, RC Reynolds, compute_ROI_stats.tcsh, level 2 (MINOR), type 5 (MODIFY)
    if ALL_LT includes an ROI value of zero, remove it

05 Aug 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add option -blip_warp_dset to input a pre-computed warp

    For example, one can import the warp from epi_b0_correct.py.


23 Jul 2024, RC Reynolds, @chauffeur_afni, level 2 (MINOR), type 4 (BUG_FIX)
    undo the the problematic -f change from 2024/04/26

    The -f was added to tcsh to prevent biowulf from updating the PATH
    when using whereami, as they have a different program with that name.
    But -f means that on macs DYLD vars would not be set, crashing afni
    when using the macos_10.12_local binaries.


25 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    deal with -Wimplicit-int, mostly from old f2c, needed for gcc-14


24 Jun 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 6 (ENHANCE)
    when running 'make', warn if CC is set (which usually causes failure)

24 Jun 2024, RC Reynolds, afni_system_check.py, level 2 (MINOR), type 6 (ENHANCE)
    display CC; warn if CPU type differs between platform and uname


20 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    stop reporting assuming TR=1.0 warnings for now

    Requested by P Taylor.

20 Jun 2024, RC Reynolds, Dimon, level 2 (MINOR), type 5 (MODIFY)
    make -read_all the default

    Basically for real-time sorting, this forces the initial processing
    of all (found) images, rather than a limited subset.  It allows for
    proper sorting without requiring an initial alphabetical aspect.


14 Jun 2024, RC Reynolds, afni-general, level 2 (MINOR), type 5 (MODIFY)
    AFNI.afnirc : use GZIP compression and turn off obliquity warnings

      AFNI_COMPRESSOR          : default to GZIP
      AFNI_AUTOGZIP            : comment out (was YES)
      AFNI_NO_OBLIQUE_WARNING  : default to YES
      AFNI_ONE_OBLIQUE_WARNING : comment out (was YES)


11 Jun 2024, RC Reynolds, build_afni.py, level 2 (MINOR), type 2 (NEW_OPT)
    backup directory removal; add -update_niivue option

    Save only most recent backup directory, possibly plus 1 containing afni.
    Add -update_niivue, and skip the operation on '-clean_root no'.


06 Jun 2024, RC Reynolds, rPkgsInstall, level 2 (MINOR), type 5 (MODIFY)
    along with 3dMVM, handle not having afni in PATH

06 Jun 2024, RC Reynolds, Makefile.macos_13_ARM, level 2 (MINOR), type 2 (NEW_OPT)
    add this Makefile (in src) for corresponding build machine

    This is a ~dupe of other_builds/Makefile.macos_13_ARM_clang.


30 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    remove unimportant anat followers from example 'publish 3d'

30 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    fix volreg TSNR for ME: use eind -> fave_echo

    Thanks to zhengchencai on MB for pointing out the problem.


25 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add -bids_deriv option

    This adds a call to P Taylor's map_ap_to_deriv.py program, to output a
    BIDS derivative tree.

25 May 2024, RC Reynolds, afni_proc.py, level 2 (MINOR), type 6 (ENHANCE)
    add -volreg_allin_warp option

    This allows specific control over 3dAllineate -warp, using a default
    of shift_rotate for rigid body registration.


24 May 2024, PD Lauren, suma, level 3 (MAJOR), type 2 (NEW_OPT)
    add alpha thresholding