#!/bin/bash -l

# Set SCC project
#$ -P PROJECT_NAME

# Give this job a name
#$ -N JOB_NAME

# 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

# Submit N jobs. Gives access to the enviormental variable $SGE_TASK_ID, which is equal to the current job number
# This example creates 3 jobs
#$ -t 1-3

# Load desired version of freesurfer
module load freesurfer/7.4.1

# create a list of inputs from the text files "subject_list.txt" and "scan_list.txt".
# These text files must be in the same directory as this file.
# Each new entry must by on a new line

readarray -t SUBJECT_LIST < "subject_list.txt"
readarray -t SCAN_LIST < "scan_list.txt"

# Set environment variables.
# INPUT_IMAGE
#   description: the full path to this subject's high resolution anatomical scan. Typically given names like "T1", "T1w", and "MEMPRAGE"
#   example: INPUT_IMAGE=/projectnb/scv/kkurkela/bids/sub-test002/ses-test002MR1/anat/sub-test002_ses-test002MR1_run-1_T1w.nii.gz
INPUT_SCAN=${SCAN_LIST[$(($SGE_TASK_ID-1))]}
# SUBJECT_ID
#   description: an arbitrary string to identify this subject
#   examples: SUBJECT_ID=sub-001
SUBJECT_ID=${SUBJECT_LIST[$(($SGE_TASK_ID-1))]}
# 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=/FULL/PATH/TO/SOME/OUTPUT/DIRECTORY

# Set recon-all variables
recon-all -all -subjid $SUBJECT_ID -i $INPUT_SCAN -parallel -openmp $NSLOTS