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slurm_proc_7T_step1.sh
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slurm_proc_7T_step1.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}
#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 $projDir
IMAGEDIR=${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_HCP.py -o /datain/bids --minmeta -s ${sub} -ss ${ses} -c dcm2niix -b --overwrite
chmod 2777 -R ${projDir}/bids
NOW=$(date +"%m-%d-%Y-%T")
echo "HeuDiConv finished $NOW" >> ${scripts}/fulltimer.txt
if [ "${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
mkdir ${based}/${version}/output/${project}
mkdir ${projDir}/bids/derivatives
cd ${projDir}
${scripts}/project_doc.sh ${project} ${subject} ${sesname} "mriqc" "no"
NOW=$(date +"%m-%d-%Y-%T")
echo "MRIQC started $NOW" >> ${scripts}/fulltimer.txt
echo "Denoising MP2RAGE with LAYNII"
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --cleanenv --bind ${projDir}/bids/sub-${sub}/ses-${ses}/anat:/datain $IMAGEDIR/laynii-2.0.0.sif /opt/laynii2/laynii/LN_MP2RAGE_DNOISE -INV1 /datain/sub-${sub}_ses-${ses}_acq-mp2rageinv_run-1_T1w.nii.gz -INV2 /datain/sub-${sub}_ses-${ses}_acq-mp2rageinv_run-2_T1w.nii.gz -UNI /datain/sub-${sub}_ses-${ses}_acq-mp2rageuni_run-3_T1w.nii.gz -beta 0.2
mv ${projDir}/bids/sub-${sub}/ses-${ses}/anat/*inv* ${projDir}/bids/derivatives/
mv ${projDir}/bids/sub-${sub}/ses-${ses}/anat/*uni_run-*_T1w.nii.gz ${projDir}/bids/derivatives/
mv ${projDir}/bids/sub-${sub}/ses-${ses}/anat/*uni_run-*_T1w.json ${projDir}/bids/derivatives/
mv ${projDir}/bids/sub-${sub}/ses-${ses}/anat/sub-${sub}_ses-${ses}_acq-mp2rageuni_run-3_T1w*border*.nii.gz ${projDir}/bids/derivatives/
mv ${projDir}/bids/sub-${sub}/ses-${ses}/anat/sub-${sub}_ses-${ses}_acq-mp2rageuni_run-3_T1w_denoised.nii.gz ${projDir}/bids/sub-${sub}/ses-${ses}/anat/sub-${sub}_ses-${ses}_acq-mp2rageunidenoised_T1w.nii.gz
mkdir ${projDir}/bids/derivatives/mriqc
chmod 777 -R ${projDir}/bids/derivatives/mriqc
mkdir ${projDir}/bids/derivatives/swi
mkdir ${projDir}/bids/derivatives/swi/${subject}
mkdir ${projDir}/bids/derivatives/swi/${subject}/${sesname}
mkdir ${projDir}/bids/derivatives/swi/${subject}/${sesname}/ndi_out
cp ${projDir}/${sub}/${ses}/*/*Aspire_P_ke_gre*/DICOM/*dcm ${projDir}/bids/derivatives/swi/${subject}/${sesname}/
cp ${projDir}/${sub}/${ses}/*/*Aspire_M_ke_gre*/DICOM/*dcm ${projDir}/bids/derivatives/swi/${subject}/${sesname}/
cp ${projDir}/${sub}/${ses}/scans/swi/*dcm ${projDir}/bids/derivatives/swi/${subject}/${sesname}/
echo "Generating QSM with hybrid Cornell-Berkeley tools"
echo "Fractional intensity threshold set to 0.3 (see scripts/matlab/ndi_qsm_fp3.sh)"
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}/bids/derivatives/swi/${subject}/${sesname}:/datain,${IMAGEDIR}/ndi:/ndi,${scripts}/matlab:/scripts ${IMAGEDIR}/matlab-r2019a.sif /scripts/ndi_qsm_fp3.sh
echo "Pseudo-BIDSifying QSM outputs"
cd ${projDir}/bids/derivatives/swi/${subject}/${sesname}
mv ./ndi_out/mag.nii ./ndi_out/${subject}_${sesname}_ndi_mag_fp3.nii
mv ./ndi_out/phs.nii ./ndi_out/${subject}_${sesname}_ndi_phs_fp3.nii
mv ./ndi_out/qsm.nii ./ndi_out/${subject}_${sesname}_ndi_qsm_fp3.nii
echo "Fractional intensity threshold set to 0.2 (see scripts/matlab/ndi_qsm_fp2.sh)"
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}/bids/derivatives/swi/${subject}/${sesname}:/datain,${IMAGEDIR}/ndi:/ndi,${scripts}/matlab:/scripts ${IMAGEDIR}/matlab-r2019a.sif /scripts/ndi_qsm_fp2.sh
echo "Pseudo-BIDSifying QSM outputs"
cd ${projDir}/bids/derivatives/swi/${subject}/${sesname}
mv ./ndi_out/mag.nii ./ndi_out/${subject}_${sesname}_ndi_mag_fp2.nii
mv ./ndi_out/phs.nii ./ndi_out/${subject}_${sesname}_ndi_phs_fp2.nii
mv ./ndi_out/qsm.nii ./ndi_out/${subject}_${sesname}_ndi_qsm_fp2.nii
echo "Fractional intensity threshold set to 0.4 (see scripts/matlab/ndi_qsm_fp4.sh)"
SINGULARITY_CACHEDIR=$CACHESING SINGULARITY_TMPDIR=$TMPSING singularity exec --bind ${projDir}/bids/derivatives/swi/${subject}/${sesname}:/datain,${IMAGEDIR}/ndi:/ndi,${scripts}/matlab:/scripts ${IMAGEDIR}/matlab-r2019a.sif /scripts/ndi_qsm_fp4.sh
echo "Pseudo-BIDSifying QSM outputs"
cd ${projDir}/bids/derivatives/swi/${subject}/${sesname}
mv ./ndi_out/mag.nii ./ndi_out/${subject}_${sesname}_ndi_mag_fp4.nii
mv ./ndi_out/phs.nii ./ndi_out/${subject}_${sesname}_ndi_phs_fp4.nii
mv ./ndi_out/qsm.nii ./ndi_out/${subject}_${sesname}_ndi_qsm_fp4.nii
cd ${projDir}
echo "Running mriqc"
TEMPLATEFLOW_HOST_HOME=$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}/
fi