#!/bin/bash -l

# Set SCC project
#$ -P drkrcs

# Give this job a name
#$ -N hipp_seg_test

# Combine output and error files into a single file
#$ -j y

# Send an email when the job finishes or if it is aborted (by default no email is sent).
#$ -m ae

# Request 4 cores for the -parellel flag.
#$ -pe omp 4

# Defaults to fair-share mem_per_core, which is at minimum 4GB.
#$ -l mem_per_core=4G

# Note:
# segmenetHA_T1.sh must be run AFTER running the recon-all routine. See segmentHA_T1.sh --help for more information.

# Load desired version of freesurfer
module load freesurfer/7.4.1

# Set environment variables.

# SUBJECT_ID
#   description: an arbitrary string to identify this subject
#   examples: SUBJECT_ID=sub-001
SUBJECT_ID=sub-001

# SUBJECTS_DIR
#   description: the full path to a directory where the output will be written. A new folder $SUBJECTS_DIR/$SUBJECT_ID will be created
#   examples: SUBJECTS_DIR=/projectnb/scv/kkurkela/bids/derivatives/freesurfer/
#   note: freesurfer will look for this variable in the enviornment. See recon-all -help
export SUBJECTS_DIR=/projectnb/scv/kkurkela/tutorial/bids/derivatives/freesurfer

# run segmentHA routine
segmentHA_T1.sh $SUBJECT_ID