NSPN_AssignLobes.sh

#!/bin/bash

#====================================================================
# Created by Kirstie Whitaker on 25th April 2016
#
# DESCRIPTION:
#    This code takes a freesurfer directory and runs the appropriate
#      commands to parcellate the volume into the six lobes defined
#      by freesurfer using the --lobesStrict flag.
#    For more information see:
#      https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation
#
# INPUTS:
#    study_dir : The directory containing the SUB_DATA folder which
#                  itself contains directories named by sub_id.
#    sub_id    : Subject ID. These folders should be inside SUB_DATA
#                  and themselves contain directories called SURFER
#                  and MPM.
#    occ       : The scan occasion. One of baseline, CBSU, UCL and
#                  WBIC. This directory contains the output of
#                  recon-all and is found inside the subject's SURFER
#                  directory.
#
# EXPECTS:
#    Recon-all and quality control edits must have been completed.
#
# OUTPUTS:
#    The following files are created inside the relavent occasion
#      directory in the subject's SURFER directory
#
#        mri/lobes+aseg.mgz
#        label/lh.lobesStrict.annot
#        label/rh.lobesStrict.annot
#
#====================================================================

#====================================================================
# USAGE: NSPN_AssignLobes.sh <study_dir> <sub> <occ>
#====================================================================
function usage {

    echo "USAGE: NSPN_AssignLobes.sh <study_dir> <sub> <occ>"
    echo "       <study_dir> is the parent directory to the SUB_DATA"
    echo "         directory and expects to find SUB_DATA inside it"
    echo "         and then the standard NSPN directory structure."
    echo "       <sub> is the subject ID that corresponds to a"
    echo "          folder in the SUB_DATA directory."
    echo "       <occ> is the scan occasion and is one of baseline,"
    echo "         CBSU, WBIC and UCL"
    echo ""
    echo "DESCRIPTION: This code takes a freesurfer directory and"
    echo "             runs the appropriate commands to parcellate"
    echo "             the volume into the six lobes defined by"
    echo "             freesurfer using the --lobesStrict flag."
    echo "             The code should be applied after recon-all"
    echo "             edits have been completed"
    exit
}

#====================================================================
# READ IN COMMAND LINE ARGUMENTS
#====================================================================
study_dir=$1
sub=$2
occ=$3

if [[ ! -d ${study_dir} ]]; then
    echo "**** STUDY DIRECTORY does not exist ****"
    usage
fi

if [[ -z ${sub} ]]; then
    echo "**** No subject ID given ****"
    usage
fi

if [[ -z ${occ} ]]; then
    echo "**** No occasion given ****"
    usage
fi

#====================================================================
# CHECK THE INPUTS
#====================================================================
surfer_dir=${study_dir}/SUB_DATA/${sub}/SURFER/${occ}

if [[ ! -d ${surfer_dir} ]]; then
    echo "Surfer dir doesn't exist - CHECK ${surfer_dir}"
    exit
fi

#====================================================================
# DEFINE VARIABLES
#====================================================================
# Set the subjects dir and subject id variables
SUBJECTS_DIR=${surfer_dir}/../
surf_sub=${occ}

#====================================================================
# PRINT TO SCREEN WHAT WE'RE DOING
#====================================================================
echo "==== Assign Lobes ===="

#====================================================================
# COMBINE LABELS
#====================================================================
# First you have to pull together the labels
# from the surface annotation files
for hemi in lh rh; do
    if [[ ! -f ${surfer_dir}/label/${hemi}.lobesStrict.annot ]]; then

        echo "  Assigning lobe labels (${hemi})"
        mri_annotation2label --subject ${surf_sub} \
                             --hemi ${hemi} \
                             --lobesStrict \
                             ${surfer_dir}/label/${hemi}.lobesStrict
    else
        echo "  ${hemi} lobe labels already assigned"
    fi
done

#====================================================================
# LABEL WHITE MATTER
#====================================================================
# Transform the surface annotation into a segmentation volume
# and label the white matter up to 5mm beneath the lobes
if [[ ! -f ${surfer_dir}/mri/lobes+aseg.mgz ]]; then

    echo "  Assigning white matter 5mm below cortical surface to lobe labes"

    mri_aparc2aseg --s ${surf_sub} \
                --labelwm \
                --rip-unknown \
                --annot lobesStrict \
                --o ${surfer_dir}/mri/lobes+aseg.mgz
else
    echo "  White matter 5mm below cortical surface already assigned to lobe"
fi

#====================================================================
# All done!
#====================================================================