/
slurm_proc_7T_CUPS_step3.sh
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/
slurm_proc_7T_CUPS_step3.sh
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#!/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=${subject:4}
if [ -d "${projDir}/bids/${subject}/${sesname}/dwi" ];
then
IMAGEDIR=${based}/singularity_images
scripts=${based}/${version}/scripts
projDir=${based}/${version}/testing/${project}
scachedir=${based}/${version}/scratch/scache/${project}/${sesname}
stmpdir=${based}/${version}/scratch/stmp/${project}/${sesname}
mkdir ${based}/${version}/scratch/scache/${project}
mkdir ${based}/${version}/scratch/stmp/${project}
mkdir ${based}/${version}/scratch/scache/${project}/${sesname}
mkdir ${based}/${version}/scratch/stmp/${project}/${sesname}
chmod 777 -R ${stmpdir}
chmod 777 -R ${scachedir}
NOW=$(date +"%m-%d-%Y-%T")
echo "QSIprep started $NOW" >> ${scripts}/fulltimer.txt
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.16.1.sif --fs-license-file /imgdir/license.txt /data/bids/sourcedata /data/bids/derivatives --freesurfer_input /data/bids/derivatives/sourcedata/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
chmod 777 -R ${projDir}/bids/derivatives/qsiprep
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} QSIprep ${based}
NOW=$(date +"%m-%d-%Y-%T")
echo "QSIprep finished $NOW" >> ${scripts}/fulltimer.txt
NOW=$(date +"%m-%d-%Y-%T")
echo "QSIprep Recon started $NOW" >> ${scripts}/fulltimer.txt
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.16.1.sif --fs-license-file /imgdir/license.txt /data/bids/sourcedata /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt_ACT-hsvs --freesurfer_input /data/bids/derivatives/sourcedata/freesurfer --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.16.1.sif --fs-license-file /imgdir/license.txt /data/bids/sourcedata /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec dsi_studio_gqi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${IMAGEDIR}:/imgdir,${stmpdir}:/paulscratch,${projDir}:/data ${IMAGEDIR}/qsiprep-v0.16.1.sif --fs-license-file /imgdir/license.txt /data/bids/sourcedata /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec amico_noddi --output-resolution 1.6 -w /paulscratch participant --participant-label ${subject}
NOW=$(date +"%m-%d-%Y-%T")
echo "QSIprep Recon finished $NOW" >> ${scripts}/fulltimer.txt
chmod 777 -R ${projDir}/bids/derivatives/qsirecon
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/qsirecon:/data ${IMAGEDIR}/matlab-R2019a.sif /work/qsinbs.sh "$subject" "$sesname"
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${scripts}:/scripts,${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datain -W /datain ${IMAGEDIR}/pylearn.sif /scripts/gqimetrics.py
SINGULARITY_CACHEDIR=${scachedir} SINGULARITY_TMPDIR=${stmpdir} singularity run --cleanenv --bind ${scripts}:/scripts,${projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi:/datanoddi ${IMAGEDIR}/neurodoc.sif /scripts/noddi_stats.sh "$subject" "$sesname"
cd {projDir}/bids/derivatives/qsirecon/${subject}/${sesname}/dwi
paste -d, *ISOVF*csv > ${subject}_${sesname}_ISOVF.csv
paste -d, *ICVF*csv > ${subject}_${sesname}_ICVF.csv
paste -d, *OD*csv > ${subject}_${sesname}_OD.csv
paste -d ${subject}_${sesname}_ICVF.csv ${subject}_${sesname}_ISOVF.csv ${subject}_${sesname}_OD.csv > ${subject}_${sesname}_NODDI_STATS.csv
${scripts}/pdf_printer.sh ${projID} ${subject} ${sesname} QSIprepRecon ${based}
fi