@SUMA_renumber_FS


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    This script is now run at the end of modern @SUMA_Make_Spec_FS
    commands, or it can be run separately for data that had been
    processed using older versions of AFNI.

    Originally written and tested on FreeSurfer (FS) v5.3 output from
    default running of 'recon-all'. This should now work for FS v6.0
    default running of 'recon-all', as well.

    Written by PA Taylor (NIMH, NIH; 2016-7).

    PURPOSE:

    This program will take the aparc+aseg.nii.gz and
    aparc.a2009s+aseg.nii.gz parcellation files produced by FreeSurfer
    (FS) and converted to NIFTI by @SUMA_Make_Spec_FS, and make the
    following related data sets (with the same prefix) for each:

        + A copy of the whole parcellation/segmentation and renumber the
          ROIs to be smaller (for colorbar representation); this file
          is called "*_REN_all.nii.gz".

        + Tissue segmentation maps (not binary, but containing the
          renumbered ROI values), based on our best guesses of of what
          each is, from both the 'mri_binarize' command in FS and our
          own supplementary reading of the ROI names. The following
          files are output:

            *_REN_gm.nii.gz    :gray matter
            *_REN_wmat.nii.gz  :white matter
            *_REN_csf.nii.gz   :cerebrospinal fluid
            *_REN_vent.nii.gz  :ventricles and choroid plexus
            *_REN_othr.nii.gz  :optic chiasm, non-WM-hypointens, etc.
            *_REN_unkn.nii.gz  :FS-defined "unknown", with voxel value >0

        + A labeltable of the new ROI values: "*_REN_all.niml.lt".
          This labeltable is attached to each of the *_REN_*.nii.gz
          files.

    RUNNING:

    At the moment, the function just takes a single, required
    argument, which is the location of the 'SUMA/' directory created
    by @SUMA_Make_Spec_FS.  The program also requires being able to
    see the two 'afni_fs_aparc+aseg_*.txt' files in the AFNI binary
    directory: that is where the information on renumbering the FS
    ROIs is).

        $ @SUMA_renumber_FS SUMA_DIR

    where SUMA_DIR is either the full or relative path to the 'SUMA/'
    directory (including that directory name).

    EXAMPLE:

        $ @SUMA_renumber_FS /data/study/SUBJ_01/FS/SUMA
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