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)  ----

24 Nov 2009, ZS Saad, afni-matlab, level 2 (MINOR), type 4 (BUG_FIX)
    Stopped writing empty attributes which caused trouble in AFNI.

    Empty attributes make AFNI halt the parsing of the header.


23 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
    Workaround for connection drop between AFNI and SUMA in Shared Memory Mode.

    Env SUMA_AttemptTalkRecover allows SUMA to recover from drop.
    This ENV is set by default to No.

23 Nov 2009, G Chen, 3dKS.R, level 2 (MINOR), type 1 (NEW_PROG)
    Kolmogorov-Smirnov test

    This is an R program that runs Kolmogrov-Smirnov test between
    two groups of subjects. It takes individual sub-brick files from
    each subject as input and spills two sub-bricks in the output,
    first one being the Kolmogorov-Smirnov statistic D, while the 2nd
    the corresponding Z-score.


20 Nov 2009, DR Glen, 3dAutomask, level 2 (MINOR), type 2 (NEW_OPT)
    apply_prefix option to save automasked input

    avoids 3dcalc step that is usually used to apply an automask.


19 Nov 2009, ZS Saad, suma, level 2 (MINOR), type 4 (BUG_FIX)
    Fixed recorder lag on OS X machines.

    On OS X platforms, the 'r' or 'R' recording modes
    used to record the previous image it seems. 


17 Nov 2009, ZS Saad, suma, level 3 (MAJOR), type 2 (NEW_OPT)
    SUMA now handles labeled datatets in a special manner

    An example of a labeled dataset would be FreeSurfer's annotation files.
    If an annotation file is present in the spec file (@SUMA_Make_Spec_FS),
    SUMA will display it as part of the background.
    You can chose to display the labeled dataset in color, contours, or both.
    Data from labeled datasets is now shown under the 'Lbl' field in the
    surface controller's Xhair block.

17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
    SUMA_AlwaysAssignSurface (see suma -environment for details)

17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
    SUMA_LabelDsetOpacity (see suma -environment for details)

17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
    SUMA_ConvexityDsetOpacity (see suma -environment for details)

17 Nov 2009, ZS Saad, suma_general, level 2 (MINOR), type 3 (NEW_ENV)
    SUMA_ShowLabelDsetAtStartup (see suma -environment for details)

17 Nov 2009, ZS Saad, ROI2dataset, level 2 (MINOR), type 2 (NEW_OPT)
    Option -label_dset creates a labeled dataset from ROIs.

    Labeled datasets are now rendered in a special manner in SUMA

17 Nov 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
    Option -dset creates a labeled dataset from annotation file.

    Labeled datasets are now rendered in a special manner in SUMA

17 Nov 2009, ZS Saad, @SUMA_Make_Spec_FS, level 2 (MINOR), type 2 (NEW_OPT)
    Script now automatically sets up the spec file with labeled datasets

    Labeled datasets are created from annotation files,
    and are now rendered in a special manner in SUMA


16 Nov 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    allow motion censoring with varying run lengths

    Also, if a max is applied in scaling, explicitly limit to [0,max].

16 Nov 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 5 (MODIFY)
    allow motion censoring with varying run lengths


09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
    Added options to check for, and correct 'bowties' in pathches.

    Bowties in patches result in non 2-manifold stiched surfaces whose
    volume cannot be caluclated. The *bowtie option deal with such cases.

09 Nov 2009, ZS Saad, SurfPatch, level 2 (MINOR), type 2 (NEW_OPT)
    Added options to shrink patch contours at nodes not in selected nodes.

    See options -adjust_contour for details.

09 Nov 2009, ZS Saad, SurfMeasures, level 2 (MINOR), type 2 (NEW_OPT)
    Added option for improved node volume estimation.

    The new measure, called node_volg, uses Gauss' Theorem to estimate
    the volume associated with a node in two isotopic surfaces. This option
    is more robust to surface curvature variations.


04 Nov 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 2 (NEW_OPT)
     3dAllineate option for motion correction

    volreg_method allows 3dAllineate, which is useful for DTI data.
    Bug fix for post-transformation matrix and dataset view


27 Oct 2009, RC Reynolds, GIFTI, level 2 (MINOR), type 2 (NEW_OPT)
    added support for optional LabelTable RGBA attributes


23 Oct 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -censor_fill and -censor_fill_par

    These options are to zero-pad TRs that were censored by 3dDeconvolve.


19 Oct 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added options for using 3dBlurInMask, instead of 3dmerge

    - added -blur_in_mask, -blur_in_automask and -blur_opts_BIM
    - added -sep_char and -subj_curly

19 Oct 2009, DR Glen, align_epi_anat.py, level 3 (MAJOR), type 2 (NEW_OPT)
    New master options, dset1/2 terminology

    New master_nnn_dxyz options to specify output resolution
    dset1 and dset2 for non-EPI/anat alignment with lpa cost function
    and turns off preprocessing steps
    giant_move option turns off resampling and changes master options
    Expanded help - including fuller description of edge method
    Removed volume registration (motion correction) for anat2epi option
    by default.
    AFNI dataset views (+orig/+acpc/+tlrc) are maintained in output
    depending on BASE, SOURCE or external dataset names for all output


14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
    Direct viewing of pre-processed datasets in Dot xform

14 Oct 2009, ZS Saad, suma, level 2 (MINOR), type 5 (MODIFY)
    New help window for Dot xform


07 Oct 2009, RW Cox, 3dBlurInMask, level 2 (MINOR), type 2 (NEW_OPT)
    Add -Mmask option to allow multiple mask values

    For independent blurring (e.g., blur WM and GM separately).


06 Oct 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
    More bug fixes related to ROI loading, and OSX's GLX problem


29 Sep 2009, RW Cox, afni, level 3 (MAJOR), type 5 (MODIFY)
    InstaCalc is more-or-less ready

    At least, I let Mike Beauchamp test it for his cunning plans.

29 Sep 2009, RC Reynolds, @Reorder, level 2 (MINOR), type 1 (NEW_PROG)
    script version of reorder plugin, for J. Bjork

29 Sep 2009, DR Glen, RetroTS, level 2 (MINOR), type 2 (NEW_OPT)
    Flexible slice timing options

    SliceOrder option allows for standard slice timing order
      alt+z, alt-z, seq+z, seq-z, Custom and 1D text file input

29 Sep 2009, DR Glen, McRetroTS, level 2 (MINOR), type 2 (NEW_OPT)
    Opt options available to compiled version

    All options available through the Opt structure are now available
    even with the compiled version of McRetroTS, making the compiled version
    functionally equivalent to the RetroTS.m version


24 Sep 2009, ZS Saad, suma, level 3 (MAJOR), type 4 (BUG_FIX)
    Fixed crashes on OS X 10.5 caused by OS X's buggy GLX implementation

24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 2 (NEW_OPT)
    Improved the 'star' blurring interface.

24 Sep 2009, ZS Saad, suma, level 2 (MINOR), type 3 (NEW_ENV)
    Setup final color blurring level.


18 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
    Added option -n minnodes

18 Sep 2009, ZS Saad, FSread_annot, level 2 (MINOR), type 2 (NEW_OPT)
    Allow specifying external FreeSurfer color table.


16 Sep 2009, RC Reynolds, 3ddot, level 2 (MINOR), type 4 (BUG_FIX)
    de-meaning data causes permission-based seg fault, apply means upon read

    Found by Giuseppe Pagnoni.


14 Sep 2009, ZS Saad, SurfClust, level 2 (MINOR), type 2 (NEW_OPT)
    Allow specifying rmm in number of edges connecting nodes.


09 Sep 2009, ZS Saad, @fast_roi, level 2 (MINOR), type 2 (NEW_OPT)
    Allow @fast_roi to accept existing TLRC transformed anatomy

09 Sep 2009, RW Cox, 3dmaskdump, level 2 (MINOR), type 2 (NEW_OPT)
    Add 'ball' options for mask generation


08 Sep 2009, DR Glen, whereami, level 2 (MINOR), type 5 (MODIFY)
    Allows MNI_ANAT space for whereami

    Subtracts 8mm I-S and uses MNI space transform to TTA

08 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
    Properly allows post-transformation matrix


04 Sep 2009, RC Reynolds, plug_realtime, level 2 (MINOR), type 2 (NEW_OPT)
    registration can now be consistent across runs

    Reg Base can be 'Current': to set the base volume from the current run
    (call this the old way), 'Current & Keep': use current run, but then
    store that base and apply it to future runs, 'External Dataset': fix the
    base from some chosen dataset.
    
    Using 'Current & Keep' makes sense for realtime registration.


03 Sep 2009, DR Glen, align_epi_anat.py, level 2 (MINOR), type 4 (BUG_FIX)
    Bug fixes for certain combinations

    Allowed BASE and SOURCE specification for oblique data
    Allowed 3dWarpDrive volume registration with mean/max base
    Removed anatomical output with oblique data and only epi2anat


26 Aug 2009, RW Cox, 3dFFT, level 2 (MINOR), type 1 (NEW_PROG)
    Compute spatial 3D FFT of a dataset

    * This is for John Butman
    * Was started a long time ago, but only finished today
    * Probably useless


25 Aug 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
    Provide keystroke fine control over cropping in image viewer

    Shift+arrowkey = scroll crop window
    Ctrl+arrowkey  = resize crop window
    Right-click on crop button = menu to set size exactly
    Hint on crop button = shows crop parameters

25 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    if volreg block, always create motion_${subj}_enorm.1D


21 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -regress_censor_motion and -regress_censor_prev

    Motivated by L Thomas and B Bones.


20 Aug 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    added motion censoring options

    Added -censor_motion, -censor_prev_TR,  -collapse_cols, -extreme_mask,
          -set_tr, -write_censor and -write_CENSORTR.
    Also modified afni_util.py, lib_afni1D.py and option_list.py.


14 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -align_epi_ext_dset, to align anat to external EPI

    This may be important for multi-channel coil EPI data with low internal
    structural contrast.  Users might align to the first (pre-steady-state)
    TR, even though that volume is not used in the analysis.


13 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -volreg_tlrc_adwarp, to apply a manual Talairach transformation


10 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    truncate min dim to 3 sig bits for -volreg_tlrc_warp/-volreg_align_e2s

    The old default was 2 bits, -volreg_warp_dxyz overrides.

10 Aug 2009, RC Reynolds, 3dSurf2Vol, level 2 (MINOR), type 5 (MODIFY)
    allow processing of -overwrite and AFNI_DECONFLICT


06 Aug 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    fixed problems found by I Mukai and K Bahadur

    - fixed -volreg_align_to base as applied in align_epi_anat.py
    - fixed blur 'averages' computation when only one run


04 Aug 2009, RC Reynolds, realtime_receiver.py, level 2 (MINOR), type 2 (NEW_OPT)
    added basic demo interface and itemized exception traps


29 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    fixed creation of extents mask when only 1 run


28 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 5 (MODIFY)
    if known, require proper slice regressor ordering in -slibase* opts


27 Jul 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 4 (BUG_FIX)
    use -slibase_sm instead of -slibase in 3dREMLfit

27 Jul 2009, RC Reynolds, 3dREMLfit, level 2 (MINOR), type 2 (NEW_OPT)
    added -slibase_sm, for slice-major ordering of regressors

    RetroTS and afni_proc.py were incorrectly using this ordering.
    ** Analysis done prior to this probably needs to be re-done.

27 Jul 2009, RC Reynolds, 1d_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -show_labels and -show_label_ordering


23 Jul 2009, RC Reynolds, timing_tool.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -partition option

23 Jul 2009, RC Reynolds, afni_run_R, level 2 (MINOR), type 5 (MODIFY)
    allow any number of args, but where first is program, last is output

23 Jul 2009, DR Glen, MEMRI models, level 2 (MINOR), type 2 (NEW_OPT)
    Single and Dual exponential models

    New models for 3dNLfim that use single and dual exponential models
    that are appropriate for MEMRI (Manganese Enhanced MRI


22 Jul 2009, RC Reynolds, realtime_reaceiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
    python replacement for serial helper

    New 'data_choice' options can be added to compute_data_for_serial_port
    for sending results of a different computation to the serial port.


21 Jul 2009, RW Cox, niml_feedme, level 2 (MINOR), type 1 (NEW_PROG)
    Test and demo program showing how to set datasets to AFNI via NIML

    An analog to rtfeedme.  Sends volumes to AFNI using VOLUME_DATA
    elements.  Pretty rudimentary.

21 Jul 2009, RW Cox, afni, level 2 (MINOR), type 5 (MODIFY)
    Update widgets and viewing when VOLUME_DATA is added to a dataset

    * Fix AFNI_setup_viewing() to update widgets properly when dataset nvals
    changes
    * Add function AFNI_update_dataset_viewing() to deal with viewing
    changes that might be needed if a dataset is altered


16 Jul 2009, ZS Saad, afni, level 2 (MINOR), type 2 (NEW_OPT)
    Added option to force autoscale on the graphing window

    The option is accessible by pressing 'A' in the graph window
    or under 'Graph->Opt->Scale->AUTO'. 

16 Jul 2009, RC Reynolds, realtime_receiver.py, level 3 (MAJOR), type 1 (NEW_PROG)
    replacement for serial_helper


14 Jul 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -max_rest, to limit the maximum duration of rest periods

14 Jul 2009, DR Glen, afni, level 2 (MINOR), type 3 (NEW_ENV)
    Added AFNI_ONE_OBLIQUE_WARNING

    AFNI_ONE_OBLIQUE_WARNING = YES makes interactive spit out ONE warning
    about obliquity per session then go quiet.


13 Jul 2009, RW Cox, 3dLocalstat, level 2 (MINOR), type 5 (MODIFY)
    OpenMP

    Also added option '-use_nonmask' to allow statistics to be computed for
    voxels not in the mask (but presumably whose neighbors are in the mask).


25 Jun 2009, RC Reynolds, Dimon, level 2 (MINOR), type 4 (BUG_FIX)
    fixed dz sent to RT plugin for oblique datasets


24 Jun 2009, RW Cox, 3dREMLfit, level 2 (MINOR), type 0 (GENERAL)
    Modify to use OpenMP more effectively.

    Have to avoid use of Doug's matrix.c functions in the main loops, since
    they do so much malloc/free, which blocks other threads from running. 
    Instead, rewrote versions of the needed functions that use pre-allocated
    workspace arrays.  Speedup is very good now for the REML setup and REML
    voxel loops.  Haven't decided whether to OpenMP-ize the GLSQ or OLSQ
    loops, since these usually take much less time.

24 Jun 2009, RC Reynolds, afni-general, level 2 (MINOR), type 4 (BUG_FIX)
    applied print changes from B Feige (26 files):

    3dfim.c afni.c afni_niml.c mri_free.c mrilib.h 3dmatmult.c NLfit_model.c
    suma_datasets.h gifti/gifti_tool.c rickr/serial_helper.c
    SUMA/  SUMA_3dSurfMask.c SUMA_ConvertSurface.c SUMA_CreateIcosahedron.c
           SUMA_Load_Surface_Object.c SUMA_MapIcosahedron.c SUMA_NikoMap.c
           SUMA_ParseCommands.h SUMA_SphericalMapping.c
           SUMA_Surf2VolCoord_demo.c SUMA_Surface_IO.c SUMA_SurfWarp.c
           SUMA_compare_surfaces.c SUMA_xColBar.c
    svm/3dsvm.c svm/3dsvm_common.c volpack/vp_octree.c


23 Jun 2009, RC Reynolds, NIFTI, level 2 (MINOR), type 4 (BUG_FIX)
    added 4 checks of alloc() returns


17 Jun 2009, RC Reynolds, afni_proc.py, level 3 (MAJOR), type 2 (NEW_OPT)
    version 2.0 : call e2a alignment and warp to standard space ready

    - mask warped EPI by its extents (at volreg step)
    - added -volreg_no_extent_mask, to block this masking
    - added 'extents' to list of mask in -mask_apply
    - change block dividers to more visual '===' with block names

17 Jun 2009, RC Reynolds, make_random_timing.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -make_3dd_contrasts and used general accuracy in block durations

17 Jun 2009, DR Glen, RetroTS.m, level 2 (MINOR), type 4 (BUG_FIX)
    Number of TRs found incorrectly because of rounding

17 Jun 2009, DR Glen, McRetroTS.m, level 2 (MINOR), type 1 (NEW_PROG)
    Matlab Compilable version of RetroTS.m

    This version calls the RetroTS function, but can be compiled
    for users that either do not have Matlab, a required toolbox
    or want to use this function in a shell script more easily.


15 Jun 2009, RC Reynolds, 3dmerge, level 2 (MINOR), type 5 (MODIFY)
    allowed short/byte datasets to use FIR blur, so no Fourier interpolation

    Also added Y/N AFNI_BLUR_INTS_AS_OLD env var to use previous method.

15 Jun 2009, DR Glen, BrikLoad.m, level 2 (MINOR), type 4 (BUG_FIX)
    Typo in BrikLoad

    Gremlin got to Pixy


11 Jun 2009, RW Cox, AlphaSim, level 2 (MINOR), type 5 (MODIFY)
    Added computation of analytic approximation of Alpha(i) for large i

    Uses a modified extreme value distribution, which looks pretty good.

11 Jun 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added masking abilities

    - in mask block, try to create anat and group masks
    - added -mask_apply option, for choosing mask to apply to regression
    - added -align_opts_aea, for extra opts to align_epi_anat.py


29 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    added -execute and now fail if block options have no corresponding blocks


28 May 2009, RC Reynolds, strblast, level 2 (MINOR), type 4 (BUG_FIX)
    partial words had resulted in skipping ahead

    found by R Notestine of UCSD

28 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 5 (MODIFY)
    example updates for AFNI_data4 and new options


27 May 2009, RC Reynolds, afni_proc.py, level 2 (MINOR), type 2 (NEW_OPT)
    updates for alignment/warp/varying run lengths

    - added -volreg_warp_dxyz option
    - if align a2e, add -no_ss to @auto_tlrc
    - for varying run lengths, fixed application of '-volreg_align_to last'
      and the -regress_est_blur_* options
      (blur estimation loops were modified for this)
    - warping to new grid truncates to 2 significant bits (if < 2 mm)