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_years 1 

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

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.


10 Mar 2008, RC Reynolds, SUMA_SurfMeasures, level 3 (MAJOR), type 4 (BUG_FIX)
    averages did not include nodes lost to -cmask

    Noticed by M Beauchamp.


05 Mar 2008, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
    Support for GIFTI surface format writing

    GIFTI writing can now be done with SUMA programs.
    For example, see options -o_gii and -xml* in ConvertSurface program.


29 Feb 2008, G Chen, 3dICA.R, level 4 (SUPER), type 1 (NEW_PROG)
    An R program that runs independent component analysis in AFNI.

    This testing program for ICA only takes one dataset that presumably has 
    already been properly pre-processed. See more details on: 
    http://afni.nimh.nih.gov/sscc/gangc/ica.html


28 Feb 2008, ZS Saad, suma-general, level 3 (MAJOR), type 3 (NEW_ENV)
    Support for GIFTI surface format reading


27 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
    Addition of p and q values under threshold bar

    Use BHelp on p and q text in suma to get more info.

27 Feb 2008, RW Cox, 3dTfitter, level 3 (MAJOR), type 2 (NEW_OPT)
    add deconvolution via the '-FALTUNG' option

    Unlike 3dDeconvolve, this deconvolution is to find the input time
    series, given the impulse response function.

27 Feb 2008, RC Reynolds, afni_history, level 4 (SUPER), type 1 (NEW_PROG)
    program to display the history of AFNI updates

    This will be used to create a web page of AFNI updates.
    Please see 'afni_history -help' for more details.


25 Feb 2008, RC Reynolds, plug_vol2surf, level 3 (MAJOR), type 4 (BUG_FIX)
    fixed application of cluster for sending data to suma

    Previously, clustering was only applied when the Olay and Thr sub-bricks
    were the same.


21 Feb 2008, RC Reynolds, GIFTI, level 4 (SUPER), type 0 (GENERAL)
    AFNI programs can now read and write GIFTI datasets

    GIFTI datasets are for data in the surface domain, with file suffix .gii.
    Support must be requested at compile time, and it requires libexpat.
    Please see http://www.nitrc.org/projects/gifti for many details.


16 Feb 2008, RW Cox, 3dTfitter, level 4 (SUPER), type 1 (NEW_PROG)
    new program = linear fits to voxel time series

    Uses L1 or L2 regression, with optional constraints to fit each voxel
    time series as a sum of basis time series, which can be 1D files or
    3D+time datasets.  Basis time series that are 1D time series are
    the same for all input voxels.  Basis time series that are 3D+time
    datasets are different for each voxel.
    Differences from 3dDeconvolve:
    * Basis time series can vary across voxels.
    * Fit coefficients can be found with L1 or L2 error functions, and
      can be constrained to be positive or negative.
    * 3dTfitter does not compute goodness-of-fit statistics.


14 Feb 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
    Graphing of dset content with 'g'

    A graph of the column content at a node can be plotted
    This would be the surface equivalent to AFNI's graphing function.
    See suma's interactive help 'ctrl+h' for more info.


06 Feb 2008, ZS Saad, SurfDist, level 3 (MAJOR), type 1 (NEW_PROG)
    Program to calculate geodesic internodal distances


23 Jan 2008, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * FDR thresh-vs-z(q) curve generation and storage in datasets.
    * Display FDR q in AFNI pval label.
    * Generate FDR curves automatically in 3dDeconvolve, and with
       '-addFDR' option in 3drefit.


12 Jan 2008, ZS Saad, suma, level 3 (MAJOR), type 0 (GENERAL)
    Scroll lists for I T and B selectors in suma

    Right click on pulldown menu titles to get
    a scroll list instead. This makes selecting from
    a long list of options, or columns, much easier.
    Right click on 'I' to the left of suma's Intensity Selection
    button for an illustration.


28 Dec 2007, RC Reynolds, gifti_tool, level 3 (MAJOR), type 1 (NEW_PROG)
    program to read and write GIFTI datasets


20 Dec 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * Clusterize reporting window.


19 Dec 2007, ZS Saad, suma-general, level 3 (MAJOR), type 0 (GENERAL)
    Use of '[i]' to select node index from surface dset

    Square bracket '[]' selection works for surface-based
    datasets much like it does for volume-based ones.
    In addition, one can use '[i]' to select the indices
    of nodes for which data are defined in a particular 
    surface-based dataset.
    For more information, see 'SUMA dataset input options:' 
    section in the output of ConvertDset -help .


03 Dec 2007, RC Reynolds, GIFTI, level 3 (MAJOR), type 0 (GENERAL)
    initial release of gifti I/O C API


20 Nov 2007, RW Cox, 3dTsort, level 3 (MAJOR), type 1 (NEW_PROG)
    new program = sorts voxel data along the time axis

    This might be useful for sorting the -stim_time_IM beta weights
    output be 3dDeconvolve.  Perhaps for something else, too?


26 Sep 2007, ZS Saad, SurfFWHM, level 4 (SUPER), type 1 (NEW_PROG)
    Program to estimate FWHM of data on surface

26 Sep 2007, ZS Saad, SurfSmooth, level 3 (MAJOR), type 5 (MODIFY)
    Big changes to data smoothing functions

    * HEAT_07 method does controlled blurring, with options
    to blur 'to' a particular FWHM. No guessing needed for
    iterative kernel bandwidth or number of iterations.
    * HEAT_05 method improved to reduce numerical precision
    problems.


20 Sep 2007, G Chen, 3dLME.R, level 4 (SUPER), type 1 (NEW_PROG)
    An R program that runs linear mixed-effects analysis at group level in AFNI.

    See more details on: http://afni.nimh.nih.gov/sscc/gangc/lme.html


31 Aug 2007, RC Reynolds, DECONFLICT, level 3 (MAJOR), type 5 (MODIFY)
    modified default behavior of programs from deconflict to no overwrite

    See AFNI_DECONFLICT in README.environment.


20 Aug 2007, RW Cox, Miscellaneous, level 3 (MAJOR), type 2 (NEW_OPT)
    Older History stuff

    * First version of '-lpc' Local Pearson Correlation cost function in
       3dAllineate.c, with rhombic dodecahedra as the default building bloks.


30 Jul 2007, RC Reynolds, regression_tests, level 3 (MAJOR), type 0 (GENERAL)
    added setup for regression testing to NIFTI package

    This can be used as a template for testing any command-line programs.