/
slurm_proc.sh
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/
slurm_proc.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}/testing
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 ${tmpdir}/${DIR} ${tmpdir}/${project}/${CLEANSUBJECT}/${session}
subject="sub-"${CLEANSUBJECT}
sesname="ses-"${session}
#check for heuristic
if [ -f "${tmpdir}/${project}/${project}_heuristic.py" ];
then
echo "trusting project heuristic"
else
cp ${scripts}/main_heuristic.py ${tmpdir}/${project}/${project}_heuristic.py
fi
if [ "${MINQC}" == "yes" ];
then
projDir=${tmpdir}/${project}
scripts=${based}/${version}/scripts
cd $projDir
IMAGEDIR=${based}/singularity_images
CACHESING=${scachedir}/${project}_${subject}_${sesname}_minqc
TMPSING=${stmpdir}/${project}_${subject}_${sesname}_minqc
mkdir $CACHESING
mkdir $TMPSING
chmod 777 -R $CACHESING
chmod 777 -R $TMPSING
NOW=$(date +"%m-%d-%Y-%T")
#heudiconv
echo "Running heudiconv"
echo "$NOW" > ${scripts}/timer.txt
ses=${sesname:4}
sub=${subject:4}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}:/datain $IMAGEDIR/heudiconv0.6.simg heudiconv -d /datain/{subject}/{session}/scans/*/DICOM/*dcm -f /datain/${project}_heuristic.py -o /datain/bids -s ${sub} -ss ${ses} -c dcm2niix -b
chmod 777 -R ${projDir}/bids
rm -rf __pycache__
mkdir ${based}/dataqc/${project}
mkdir ${projDir}/bids/derivatives
cd ${projDir}
rm ${projDir}/bids/derivatives/mriqc
mkdir ${projDir}/bids/derivatives/mriqc
chmod 2777 -R ${projDir}/bids/derivatives/mriqc
cd $projDir
echo "Running mriqc"
NOW=$(date +"%m-%d-%Y-%T")
echo "$NOW" >> ${scripts}/timer.txt
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv --bind ${projDir}/bids:/data --bind ${projDir}/bids/derivatives/mriqc:/out $IMAGEDIR/mriqc-0.16.0.sif /data /out participant --participant-label ${sub} --session-id ${ses} --fft-spikes-detector --despike --no-sub
chmod 2777 -R ${projDir}/bids/derivatives/mriqc
NOW=$(date +"%m-%d-%Y-%T")
echo "$NOW" >> ${scripts}/timer.txt
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} mriqc ${based}
rm -rf $CACHESING
rm -rf $TMPSING
mv ${projDir}/bids/derivatives/mriqc ${based}/dataqc/${project}/mriqc
chmod 777 -R ${based}/dataqc/${project}
else
projDir=${tmpdir}/${project}
scripts=${based}/${version}/scripts
cd $projDir
rm -rf ${projDir}/bids/derivatives/mriqc/*${subject}*
rm -rf ${projDir}/bids/derivatives/mriqc/${subject}
rm -rf ${projDir}/bids/derivatives/fmriprep/${subject}
rm -rf ${projDir}/bids/derivatives/fmriprep/*${subject}*
rm -rf ${projDir}/bids/derivatives/freesurfer/${subject}
rm -rf ${projDir}/bids/derivatives/xcp/${sesname}/xcp_despike/${subject}
rm -rf ${projDir}/bids/derivatives/xcp/${sesname}/xcp_scrub/${subject}
rm -rf ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}
rm -rf ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}
rm -rf ${projDir}/bids/derivatives/qsiprep/${subject}
rm -rf ${projDir}/bids/derivatives/qsiprep/*${subject}*
rm -rf ${projDir}/bids/derivatives/qsirecon/${subject}
rm -rf ${projDir}/bids/derivatives/qsirecon/*${subject}*
rm -rf ../../output/${project}/${subject}/${sesname}
IMAGEDIR=${based}/singularity_images
CACHESING=${scachedir}/${project}_${subject}_${sesname}_dcm2rsfc
TMPSING=${stmpdir}/${project}_${subject}_${sesname}_dcm2rsfc
mkdir $CACHESING
mkdir $TMPSING
NOW=$(date +"%m-%d-%Y-%T")
echo "HeuDiConv started $NOW" > ${scripts}/fulltimer.txt
#heudiconv
echo "Running heudiconv"
${scripts}/project_doc.sh ${project} ${subject} ${sesname} "heudiconv" "yes"
ses=${sesname:4}
sub=${subject:4}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${projDir}:/datain ${IMAGEDIR}/heudiconv-0.9.0.sif heudiconv -d /datain/{subject}/{session}/*/SCANS/*/DICOM/*dcm -f /datain/${project}_heuristic.py -o /datain/bids -s ${sub} -ss ${ses} -c dcm2niix -b --overwrite --minmeta
chmod 2777 -R ${projDir}/bids
#rm -rf __pycache__
#rm -rf $CACHESING/*
#rm -rf $TMPSING/*
NOW=$(date +"%m-%d-%Y-%T")
echo "HeuDiConv finished $NOW" >> ${scripts}/fulltimer.txt
#jsoncrawler.sh runs once, for all sessions
if [ "${fieldmaps}" == "yes" ];
then
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}:/data,${scripts}:/scripts ${IMAGEDIR}/ubuntu-jq-0.1.sif /scripts/jsoncrawler.sh /data/bids ${sesname} ${subject}
fi
rm ${projDir}/bids/derivatives/${subject}/${sesname}/tmp
rm ${projDir}/bids/derivatives/${subject}/${sesname}/test.txt
dirs=$(ls ${projDir}/${sub}/${ses}/*/SCANS/*/*/*secondary*xml)
dirp=${dirs%/DICOM/*secondary*xml}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${scripts}:/scripts,${dirp}:/datain ${IMAGEDIR}/bidscoin.sif python /scripts/detectphysiolog.py
physdir=$(ls ${projDir}/${sub}/${ses}/*/SCANS/*/*/*physio*dcm)
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}/bids/${subject}/${sesname}/func:/datadir,${physdir}:/datain/${subject}_${sesname}_task-rest_dir-PA_run-1_physio.dcm ${IMAGEDIR}/bidsphysio.sif physio2bidsphysio --infile /datain/${subject}_${sesname}_task-rest_dir-PA_run-1_physio.dcm --bidsprefix /datadir/${subject}_${sesname}_task-rest_dir-PA_run-1
chmod 777 -R ${projDir}/bids/${subject}/${sesname}
mv ${projDir}/bids/${subject}/${sesname}/func/${subject}_${sesname}_task-rest_dir-PA_run-1_recording-external_trigger_physio.json ${projDir}/bids/${subject}/${sesname}/func/${subject}_${sesname}_task-rest_dir-PA_run-1_recording-externaltrigger_physio.json
mv ${projDir}/bids/${subject}/${sesname}/func/${subject}_${sesname}_task-rest_dir-PA_run-1_recording-external_trigger_physio.tsv.gz ${projDir}/bids/${subject}/${sesname}/func/${subject}_${sesname}_task-rest_dir-PA_run-1_recording-externaltrigger_physio.tsv.gz
echo "*_physio.*" > ${projDir}/bids/.bidsignore
mkdir ${based}/${version}/output/${project}
mkdir ${projDir}/bids/derivatives
cd ${projDir}
mkdir ${projDir}/bids/derivatives/mriqc
chmod 777 -R ${projDir}/bids/derivatives/mriqc
cd $projDir
echo "Running mriqc"
${scripts}/project_doc.sh ${project} ${subject} ${sesname} "mriqc" "no"
NOW=$(date +"%m-%d-%Y-%T")
echo "MRIQC started $NOW" >> ${scripts}/fulltimer.txt
TEMPLATEFLOW_HOST_HOME=$IMAGEDIR/templateflow
export SINGULARITYENV_TEMPLATEFLOW_HOME="/templateflow"
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --bind ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME},${projDir}/bids:/data,${projDir}/bids/derivatives/mriqc:/out $IMAGEDIR/mriqc-0.16.1.sif /data /out participant --participant-label ${sub} --session-id ${ses} -v --fft-spikes-detector --despike --no-sub
chmod 2777 -R ${projDir}/bids/derivatives/mriqc
NOW=$(date +"%m-%d-%Y-%T")
echo "MRIQC finished $NOW" >> ${scripts}/fulltimer.txt
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} mriqc ${based}
#rm -rf ${TMPSING}/*
#rm -rf ${CACHESING}/*
mkdir ${dataqc}/${project}
cp -R ${projDir}/bids/derivatives/mriqc ${dataqc}/${project}/
NOW=$(date +"%m-%d-%Y-%T")
echo "fMRIPrep started $NOW" >> ${scripts}/fulltimer.txt
#fmriprep
echo "Running fmriprep on $subject $sesname"
#add more details of fMRIPrep arguments if necessary
${scripts}/project_doc.sh ${project} ${subject} ${sesname} "fmriprep" "no"
if [ "${longitudinal}" == "yes" ];
then
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME},$IMAGEDIR/license.txt:/opt/freesurfer/license.txt,$TMPSING:/paulscratch,${projDir}:/datain $IMAGEDIR/fmriprep-20.2.1.sif fmriprep /datain/bids /datain/bids/derivatives participant --participant-label ${subject} --longitudinal --output-spaces {MNI152NLin2009cAsym,T1w,fsnative} --use-aroma -w /paulscratch --fs-license-file /opt/freesurfer/license.txt
elif [ "${longitudinal}" == "no" ];
then
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${TEMPLATEFLOW_HOST_HOME}:${SINGULARITYENV_TEMPLATEFLOW_HOME},$IMAGEDIR/license.txt:/opt/freesurfer/license.txt,$TMPSING:/paulscratch,${projDir}:/datain $IMAGEDIR/fmriprep-20.2.1.sif fmriprep /datain/bids /datain/bids/derivatives participant --participant-label ${subject} --output-spaces {MNI152NLin2009cAsym,T1w,fsnative} --use-aroma -w /paulscratch --fs-license-file /opt/freesurfer/license.txt
fi
NOW=$(date +"%m-%d-%Y-%T")
echo "fMRIPrep finished $NOW" >> ${scripts}/fulltimer.txt
#rm -rf ${TMPSING}/*
#rm -rf ${CACHESING}/*
chmod 2777 -R ${projDir}/bids/derivatives/fmriprep
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} fmriprep ${based}
#ASHS
#export SINGULARITYENV_ASHS_ROOT=/opt/ashs/ashs-1.0.0
#SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${projDir}:/datain $IMAGEDIR/ashs-1.0.0.sif $SINGULARITYENV_ASHS_ROOT/bin/ashs_main.sh -a /opt/ashs/ashs_atlas_upennpmc_20161128 -g /datain/bids/${subject}/${sesname}/anat/${subject}_${sesname}_T1w.nii.gz -f /datain/bids/${subject}/${sesname}/anat/${subject}_${sesname}_acq-highreshippocampus_run-1_T2w.nii.gz -w /datain/bids/derivatives/ashs/${subject}/${sesname}
if [ -d "${projDir}/bids/${subject}/${sesname}/func" ];
then
#copy freesurfer to fmriprep so xcpEngine can find it
cd ${projDir}/bids/derivatives
mkdir ./fmriprep/freesurfer
cp -R ./freesurfer/fsaverage ./fmriprep/freesurfer/fsaverage
cp -R ./freesurfer/${subject} ./fmriprep/freesurfer/${subject}
chmod 2777 -R ${projDir}/bids/derivatives/fmriprep
cd ${projDir}
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p started $NOW" >> ${scripts}/fulltimer.txt
#generate xcpEngine cohorts for a new subject
${scripts}/func_cohort_maker.sh ${subject} ${sesname} yes
#xcpEngine 36p
$scripts/project_doc.sh ${project} ${subject} ${sesname} "xcpengine" "no"
cp ${scripts}/xcpEngineDesigns/*_gh.dsn ${projDir}/
cd ${projDir}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv -B ${projDir}:/data,$TMPSING:/tmpdir $IMAGEDIR/xcpengine-1.2.3.sif -d /data/fc-36p_gh.dsn -c /data/cohort_func_${subject}_${sesname}.csv -o /data/bids/derivatives/xcp/${sesname}/xcp_minimal_func -r /data/bids -i /tmpdir
chmod 2777 -R ${projDir}/bids/derivatives/xcp*
mv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/*quality.csv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/${subject}_${sesname}_quality_fc36p.csv
${scripts}/procd.sh ${project} xcp no ${subject} ${based}
#make different project_doc conditions for different xcpEngine dsns
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} xcp36p ${based}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --bind ${scripts}/spm12:/spmtoolbox,${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/xcp/${sesname}:/datain ${IMAGEDIR}/matlab-R2019a.sif /work/rsfcnbs.sh "xcp_minimal_func" "${subject}"
mkdir ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs
mkdir ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/fc36p
chmod 777 -R ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/fc36p
cp ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/*txt ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/fc36p/
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p finished $NOW" >> ${scripts}/fulltimer.txt
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p despike started $NOW" >> ${scripts}/fulltimer.txt
#xcpEngine 36p despike
$scripts/project_doc.sh ${project} ${subject} ${sesname} "xcpengine" "no"
cd ${projDir}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv -B ${projDir}:/data,$TMPSING:/tmpdir $IMAGEDIR/xcpengine-1.2.3.sif -d /data/fc-36p_despike_gh.dsn -c /data/cohort_func_${subject}_${sesname}.csv -o /data/bids/derivatives/xcp/${sesname}/xcp_despike -r /data/bids -i /tmpdir
chmod 2777 -R ${projDir}/bids/derivatives/xcp*
mv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_despike/${subject}/*quality.csv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/${subject}_${sesname}_quality_despike.csv
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --bind ${scripts}/spm12:/spmtoolbox,${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/xcp/${sesname}:/datain ${IMAGEDIR}/matlab-R2019a.sif /work/rsfcnbs.sh "xcp_despike" "${subject}"
mkdir ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/despike
chmod 777 -R ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/despike
cp ${projDir}/bids/derivatives/xcp/${sesname}/xcp_despike/${subject}/fcon/*txt ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/despike/
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p despike finished $NOW" >> ${scripts}/fulltimer.txt
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p_scrub started $NOW" >> ${scripts}/fulltimer.txt
#xcpEngine 36p_scrub
cd ${projDir}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv -B ${projDir}:/data,$TMPSING:/tmpdir $IMAGEDIR/xcpengine-1.2.3.sif -d /data/fc-36p_scrub_gh.dsn -c /data/cohort_func_${subject}_${sesname}.csv -o /data/bids/derivatives/xcp/${sesname}/xcp_scrub -r /data/bids -i /tmpdir
chmod 2777 -R /projects/BICpipeline/Pipeline_Pilot/TestingFork/${project}/bids/derivatives/xcp*
mv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_scrub/${subject}/*quality.csv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/${subject}_${sesname}_quality_scrub.csv
${scripts}/pdf_printer.sh ${project} ${subject} ${sesname} xcp36pscrub ${based}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv --bind ${scripts}/spm12:/spmtoolbox,${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/xcp/${sesname}:/datain ${IMAGEDIR}/matlab-R2019a.sif /work/rsfcnbs.sh "xcp_scrub" "${subject}"
mkdir ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/scrub
chmod 777 -R ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/scrub
cp ${projDir}/bids/derivatives/xcp/${sesname}/xcp_scrub/${subject}/fcon/*txt ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/nbs/scrub/
# rm ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_func/${subject}/fcon/*txt
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-36p_scrub finished $NOW" >> ${scripts}/fulltimer.txt
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-aroma started $NOW" >> ${scripts}/fulltimer.txt
#xcpEngine aroma
$scripts/project_doc.sh ${project} ${subject} ${sesname} "xcpengine" "no"
cd ${projDir}
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv -B ${projDir}:/data,$TMPSING:/tmpdir $IMAGEDIR/xcpengine-1.2.3.sif -d /data/fc-aroma_gh.dsn -c /data/cohort_func_${subject}_${sesname}.csv -o /data/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma -r /data/bids -i /tmpdir
chmod 2777 -R ${projDir}/bids/derivatives/xcp*
mv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/*quality.csv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/${subject}_${sesname}_quality_aroma.csv
${scripts}/procd.sh $project xcp no ${subject} ${based}
cp ${scripts}/projdoc.css ${based}/batchproc/${project}/${project}_sample.css
NOW=$(date +"%m-%d-%Y-%T")
echo "xcpEngine fc-aroma finished $NOW" >> ${scripts}/fulltimer.txt
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity run --cleanenv --bind ${scripts}/spm12:/spmtoolbox,${scripts}/matlab:/work,${scripts}/2019_03_03_BCT:/bctoolbox,${projDir}/bids/derivatives/xcp/${sesname}:/datain ${IMAGEDIR}/matlab-R2019a.sif /work/rsfcnbs.sh "xcp_minimal_aroma" "${subject}"
mkdir ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/fcon/nbs
chmod 777 -R ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/fcon/nbs
mv ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/fcon/*txt ${projDir}/bids/derivatives/xcp/${sesname}/xcp_minimal_aroma/${subject}/fcon/nbs/
#rm -rf ${CACHESING}/*
#rm -rf ${TMPSING}/*
if [ -d "${projDir}/bids/${subject}/${sesname}/dwi" ];
then
IMAGEDIR=${based}/singularity_images
scripts=${based}/${version}/scripts
projDir=${based}/${version}/testing/${project}
scachedir=${based}/${version}/scratch/scache/${project}/${subject}/${sesname}
stmpdir=${based}/${version}/scratch/stmp/${project}/${subject}/${sesname}
mkdir ${based}/${version}/scratch/scache/${project}
mkdir ${based}/${version}/scratch/stmp/${project}
mkdir ${based}/${version}/scratch/scache/${project}/${subject}
mkdir ${based}/${version}/scratch/stmp/${project}/${subject}
mkdir ${scachedir}
mkdir ${stmpdir}
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-v0.13.0RC2.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --output-resolution 2.5 -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-v0.13.0RC2.sif --fs-license-file /imgdir/license.txt /data/bids /data/bids/derivatives --recon_input /data/bids/derivatives/qsiprep --recon_spec mrtrix_multishell_msmt --output-resolution 2.5 -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"
${scripts}/pdf_printer.sh ${projID} ${subject} ${sesname} QSIprepRecon ${based}
fi
fi
${scripts}/pipeline_collate.sh -p ${project} -z ${subject} -s ${sesname} -b ${based} -t beta
fi
cd ${projDir}
NOW=$(date +"%m-%d-%Y")
mkdir ./tars
chmod 777 -R ./tars
tar -czf ./tars/${sub}_${ses}_${NOW}.tar.gz ./*"${sub}"*_*${ses}* ./bids/*"${sub}"* ./bids/derivatives/*/*${sub}* ./bids/derivatives/xcp/ses-"${ses}"/*/*${sub}* ../../data_qc/${project}/*${sub}*${ses}* ../../output/${project}/*${sub}*
chmod 777 ./tars/${sub}_${ses}_${NOW}.tar.gz