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 3 -past_months 6 

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

29 Sep 2008, RC Reynolds, 3dmatmult, level 3 (MAJOR), type 1 (NEW_PROG)
    program to multiply AFNI datasets slice-by-slice as matrices


29 Aug 2008, ZS Saad, ExamineXmatR, level 3 (MAJOR), type 1 (NEW_PROG)
    An interactive tool to examine a design matrix


28 Aug 2008, RW Cox, 3dAllineate, level 3 (MAJOR), type 5 (MODIFY)
    A number of changes to improve robustness.

    * Don't smooth noise added to source image outside of the mask
    * Reduce default smoothing level for -lpc in coarse pass
    * Increase number of points used for matching in the coarse pass
    * More refinements of the twobest results in the coarse pass
    * Refinements (-num_rtb option) of the twobest results in the fine pass
    All this adds CPU time, but seems to make the program more reliably
    convergent.  Also:
    * Restored operation of the -check option, to restart the optimization
      at the final solution with other methods, to see what results they
      give compared to the original method.


21 Aug 2008, RW Cox, 3dREMLfit, level 4 (SUPER), type 1 (NEW_PROG)
    Program to mimic 3dDeconvolve, but with serial correlations

    Uses ARMA(1,1) model of noise, separately for each voxel.


10 Jul 2008, RC Reynolds, plug_realtime, level 3 (MAJOR), type 5 (MODIFY)
    receive oblique transform matrix via new OBLIQUE_XFORM interface

10 Jul 2008, RC Reynolds, Dimon, level 3 (MAJOR), type 5 (MODIFY)
    if the data is oblique, pass the transformation matrix to plug_realtime


27 Jun 2008, RC Reynolds, gen_epi_review.py, level 3 (MAJOR), type 1 (NEW_PROG)
    generate afni/drive_afni script to review initial EPI data

    This program was written to be called from the afni_proc.py output script.


11 Jun 2008, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 5 (MODIFY)
    Obliquity handling in alignment, more grid options


09 May 2008, ZS Saad, 3dROIstats, level 3 (MAJOR), type 2 (NEW_OPT)
    Added option -1Dformat to output results in 1D format


08 May 2008, ZS Saad, 3dsvm, level 3 (MAJOR), type 4 (BUG_FIX)
    Fixed memory corruption caused by improper declaration of combName


07 May 2008, RC Reynolds, make_random_timing.py, level 3 (MAJOR), type 1 (NEW_PROG)
    generate random stimulus timing files

    This generates random timing files suitable for use in 3dDeconvolve.
    The timing is not restricted to a TR grid, though that is possible.
    Consider use with '3dDeconvolve -nodata'.


07 Apr 2008, DR Glen, align_epi_anat.py, level 4 (SUPER), type 1 (NEW_PROG)
    Alignment of EPI and Anatomical datasets

    Aligns anat and EPI data. Alignment is in either direction of anat to
    epi or epi to anat. Transformations are combined where possible as
    from time series registration and talairach transformations. Multiple
    child epi datasets may be aligned at the same time.