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


1) This script creates one new dset in the SUMA/ directory, called
fs_parc_wb_mask.nii.gz.  This dset is a whole brain mask based on the
FS parcellation.  Note that this is *different* than the
brainmask.nii* dset that FS creates.  This mask is created in the
following way:

    + binarize aparc+aseg_REN_all.nii.*
    + inflate by 2 voxels (3dmask_tool)
    + infill holes (3dmask_tool)
    + erode by 2 voxels (3dmask_tool)

The final mask seems much more specific to the brain structure than
brainmask.nii*.  It also removes several small gaps and holes in the
parcellation dset.  In general, it seems like quite a useful whole
brain mask.

2) This script also 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 the fs_parc_wb_mask.nii.gz dset that
                  this script has created (see details just above).

    qc_02*.jpg  : the overlay is a set of tissues, like a segmentation
                  map of 4 classes:
                        red    - GM - red
                        blue   - WM
                        green  - ventricles
                        violet - CSF+other+unknown
                  (from the *REN* files made by AFNI/SUMA).

    qc_03*.jpg  : the GM only

    qc_04*.jpg  : the WM only

    qc_05*.jpg  : the overlay is the "2000" atlas parcellation (from
                  the file: aparc+aseg*REN*all*)


adjunct_suma_fs_mask_and_qc             \
    -sid       sub-001                  \
    -suma_dir  group/sub-001/SUMA