adjunct_suma_fs_roi_info

OVERVIEW

In brief, this script is for quickly making some ROI stats (counts)
for the SUMA/ directory created by @SUMA_Make_Spec_FS after running
FreeSurfer's recon-all.

This program should be used *after* running adjunct_suma_fs_mask_and_qc,
which makes a useful mask from the aparc+aseg dataset, called
fs_parc_wb_mask.nii.gz.

written by PA Taylor.

# --------------------------------------------------------------------

USAGE

This program has the following options:

    -sid          SUBJ_ID    :(req) subject ID

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

    -help                    :(opt) show help

    -hview                   :(opt) show help in text editor

    -ver                     :(opt) show version

OUTPUT

This script makes four *.1D files in the specified SUMA/ directory.
Column labels are present in each file.  Note there are 2 ways to
think of brain volumes after running FS's recon-all: the
brainmask.nii* file (= br_mask), or the number of voxels in the full
set of the aseg/aparc dset for a given atlas (= "all" segment, from
the *_REN_all.nii* dset).

    Nvox                    : number of voxels in the ROI, segment or
                              mask. This number is always an integer,
                              >= 0.

    FR_BR_MASK              : fraction of the number of voxels, segment
                              or mask, relative to the "br_mask" dset
                              (that is, to the brainmask.nii* volume).

    FR_PARC_MASK            : fraction of the number of voxels, segment
                              or mask, relative to the "parc_mask" dset
                              (that is, to the fs_parc_wb_mask.nii.gz
                              volume that is created by the AFNI program
                              adjunct_suma_fs_mask_and_qc).  If this file
                              does not exist, you will get a col of -1
                              values for the fraction;  but you *should*
                              just run adjunct_suma_fs_mask_and_qc.

                              fs_parc_wb_mask.nii.gz is a filled in
                              form of the aparc+aseg segmentation result.

    FR_ALL_ROI              : fraction of the number of voxels, segment
                              or mask, relative to the full set of ROIs
                              in the given parcellation (that is, to the
                              *REN_all.nii* volume).

Note that the ROI string labels are provided for each ROI, but behind
a comment symbol in each line (so you can use them as regular *.1D
files, with 1dcat, 1dtranspose, etc.).

  stats_fs_rois_2000_FT.1D  : info for the "2000" parcellation
                              (from the file: aparc+aseg_REN_all.nii*)

  stats_fs_rois_2009_FT.1D  : info for the "2009" parcellation
                              (from the file: aparc+aseg_REN_all.nii*)

  stats_fs_segs_2000_FT.1D  : info for the "2000" parc brain mask
                              and tissue/segmentations (from the
                              brainmask.nii* and aparc+aseg_REN_* files)

  stats_fs_segs_2009_FT.1D  : info for the "2009" parc brain mask
                              and tissue/segmentations (from the
                              brainmask.nii* and aparc.a2009s+aseg_REN_*
                              files)

EXAMPLE

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