adjunct_suma_fs_rois.tcsh


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.

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 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  : voxel counts of the "2000" parcellation
                              (from the file: aparc+aseg_REN_all.nii*)

  stats_fs_rois_2009_FT.1D  : voxel counts of the "2009" parcellation
                              (from the file: aparc+aseg_REN_all.nii*)

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

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

EXAMPLE

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