In brief, this script is for quickly making some QC images for the
SUMA/ directory created by @SUMA_Make_Spec_FS after running
FreeSurfer's recon-all.  Phew, we made it.

written by PA Taylor.

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This program has the following options:

    -sid          SUBJ_ID    :(req) subject ID

    -suma_dir     SUMA_DIR   :(req) SUMA/ directory output by AFNI's

    -no_clean                :(opt) do not remove temporary working
                              subdirectory (def: remove it)

    -help                    :(opt) show help

    -hview                   :(opt) show help in text editor

    -ver                     :(opt) show version


This script makes three *.jpg files in the specified SUMA/
directory. The underlay in each is the *SurfVol.nii* dset.  Each JPG
is row of axial, sagittal and coronal montages around the volumes
defined by the brainmask.nii*:

    qc_00*.jpg  : the overlay is the brainmask.nii* volume in red, and
                  the subset of that volume that was parcellated by FS
                  (in either the "2000" or "2009" atlases) is outlined
                  in black.

                  The idea for this formatting is that we do want to
                  see the official FS brainmask, but we might also
                  want to note its differences with the the binarized
                  aparc+aseg file.  We might prefer using one or the
                  other dsets as a mask for other work.

    qc_01*.jpg  : the overlay is a set of tissues, like a segmentation
                  map of 4 classes: GM, WM, ventricles, and then
                  CSF+other+unknown (from the *REN* files made by

    qc_02*.jpg  : the overlay is the "2000" atlas parcellation (from
                  the file: aparc+aseg*REN*all*)


adjunct_suma_fs_qc.tcsh                 \
    -sid       sub-001                  \
    -suma_dir  group/sub-001/SUMA