slurm_proc_7T_ashs.sh

#!/bin/bash
#slurm_process_pipeline.sh

while getopts :p:s:z:m:f:l:b:t: option; do
	case ${option} in
    	p) export CLEANPROJECT=$OPTARG ;;
    	s) export CLEANSESSION=$OPTARG ;;
    	z) export CLEANSUBJECT=$OPTARG ;;
	m) export MINQC=$OPTARG ;;
	f) export fieldmaps=$OPTARG ;;
	l) export longitudinal=$OPTARG ;;
	b) export based=$OPTARG ;;
	t) export version=$OPTARG ;;
	esac
done
## takes project, subject, and session as inputs

pilotdir=${based}/original_location_of_images_from_XNAT
IMAGEDIR=${based}/singularity_images
tmpdir=${based}/${version}/testing
scripts=${based}/${version}/scripts
bids_out=${based}/${version}/bids_only
conn_out=${based}/${version}/conn_out
dataqc=${based}/${version}/data_qc
stmpdir=${based}/${version}/scratch/stmp
scachedir=${based}/${version}/scratch/scache

cd $pilotdir

DIR=${CLEANPROJECT}/${CLEANSUBJECT}/${CLEANSESSION}


## setup our variables and change to the session directory

echo ${CLEANPROJECT}
echo ${CLEANSUBJECT}
echo ${CLEANSESSION}
pwd

#translating naming conventions
echo "${CLEANSESSION: -1}"
session="${CLEANSESSION: -1}"
echo ${session}
project=${CLEANPROJECT}
mkdir -p ${tmpdir}/${project}/${CLEANSUBJECT}/${session}
cp -R ${pilotdir}/${DIR} ${tmpdir}/${project}/${CLEANSUBJECT}/${session}

subject="sub-"${CLEANSUBJECT}
sesname="ses-"${session}

	projDir=${tmpdir}/${project}
	scripts=${based}/${version}/scripts

	cd $projDir

	IMAGEDIR=${based}/singularity_images
	CACHESING=${scachedir}/${project}_${subject}_${sesname}_dcm2rsfc
	TMPSING=${stmpdir}/${project}_${subject}_${sesname}_dcm2rsfc
	mkdir $CACHESING
	mkdir $TMPSING

        ses=${sesname:4}
	sub=${subject:4}

	export SINGULARITYENV_ASHS_ROOT=/opt/ashs/ashs-1.0.0
	SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${projDir}:/datain $IMAGEDIR/ashs-1.0.0.sif $SINGULARITYENV_ASHS_ROOT/bin/ashs_main.sh -a /opt/ashs/ashs_atlas_umcutrecht_7t_20170810 -g /datain/bids/${subject}/${sesname}/anat/${subject}_${sesname}_acq-mp2rageunidenoised_T1w.nii.gz -f /datain/bids/${subject}/${sesname}/anat/${subject}_${sesname}_acq-highreshippocampus_run-1_T2w.nii.gz -w /datain/bids/derivatives/ashs/${subject}/${sesname}