First commit

.gitignore

+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db

README.txt

+-----------------------------------------------
+dHCP neonatal dMRI data processing pipeline
+March, 2018
+
+V 0.0.1: Pipeline reflecting the first data release processing
+-----------------------------------------------
+Comprehensive and automated pipeline to consistently analyse neonatal dMRI data from the developing Human Connectome Project (dHCP).
+
+If you use the pipeline in your work, please cite the following article:
+Bastiani, M., Andersson, J., Cordero-Grande, L., Murgasova, M., Hutter, J., Price, A.N., Makropoulos, A., Fitzgibbon, S.P., Hughes, E., Rueckert, D., Victor, S., Rutherford, M., Edwards, A.D., Smith, S., Tournier, J.-D., Hajnal, J.V., Jbabdi, S., Sotiropoulos, S.N. (2018). Automated processing pipeline for neonatal diffusion MRI in the developing Human Connectome Project. NeuroImage. 
+
+
+Installation
+------------
+The pipeline consists of several bash scripts.
+Once it has been downloaded, the first thing to do is fill the correct paths into:
+dHCP_neo_dMRI_setup.sh
+
+The script needs to be run before launching the processing jobs.
+
+
+-------------------------------------------
+Examples
+-------------------------------------------
+To launch the pipeline for a single subject, use the following command:
+${scriptsFolder}/dHCP_neo_dMRI_setJobs.sh ${rawDataFolder}/sub-${cid} ses-${no} ${rawDataFile} ${cid} ${scriptsFolder}/dhcp300_f.txt ${outFolder} ${age} ${birth} ${n_sessions}
+
+This command will submit all the necessary scripts to process the raw dMRI data. The necessary inputs are:
+${rawDataFolder}/sub-${cid}: Path to raw data
+ses-${no}: Session number
+${rawDataFile}: Raw data file name
+${cid}: Connectome ID
+${scriptsFolder}/dhcp300_f.txt: Protocol file
+${outFolder}: Output folder
+${age}: Age at scan (in rounded weeks)
+${birth}: Age at birth (in rounded weeks)
+${n_sessions}: Total number of scanning sessions for the same subject
+
+
+-------------------------------------------
+Non-dHCP data
+-------------------------------------------
+To convert a locally acquired dataset such that it can be used with the pipeline, use the command:
+${scriptsFolder}/utils/getProtocol
+
+By typing the command in a terminal, the necessary inputs will be shown.
+The script will generate a raw data file and a protocol file that can be used with the pipeline.
+

dHCP_neo_dMRI_importFiles.sh

+#!/bin/bash
+
+
+set -e
+echo -e "\n START: Importing files"
+
+# scriptsFolder=/home/fs0/matteob/scripts/dHCP
+
+if [ "$6" == "" ];then
+    echo ""
+    echo "usage: $0 <Data folder> <Data filename> <Output preprocessing folder> <Acquisition protocol> <Number of volumes> <Number of b0s>"
+    echo "       Data folder: Path to the data file"
+    echo "       Data filename: File name for the raw data"
+    echo "       Output preprocessing folder: Path to the output pre-processing folder"
+    echo "       Acqusition protocol: Text file with acquisition parameters"
+    echo "       Number of volumes: Number of acquired volumes"
+    echo "       Number of b0s: Number of b0s from each phase encoding block to use when estimating the fieldmap"
+    echo ""
+    exit 1
+fi
+
+
+dataFolder=$1      # Path to data file
+dataFile=$2        # Data file name
+prepFolder=$3   # Output folder
+acqProt=$4         # Acquisition protcol
+nVols=$5           # Number of acquired volumes
+noB0s=$6           # Number of B0 volumes for each PE direction used to estimate distortions with TOPUP
+
+
+#============================================================================
+# Separate b0 volumes according to their PE direction and obtain 
+# bvals and bvecs files. Round bvals to identify shells.
+#============================================================================
+idxLR=0
+idxRL=0
+idxAP=0
+idxPA=0
+LRvols=-1
+RLvols=-1
+APvols=-1
+PAvols=-1
+no_LR=0
+no_RL=0
+no_AP=0
+no_PA=0
+idxb400=0
+idxb1000=0
+idxb2600=0
+i=0
+
+echo -n > ${prepFolder}/eddy/eddyIndex.txt
+while read line; do
+    bvec_x[i]=`echo $line | awk {'print $1'}`
+    bvec_y[i]=`echo $line | awk {'print $2'}`
+    bvec_z[i]=`echo $line | awk {'print $3'}`
+    bval[i]=`echo $line | awk {'print $4'}`
+    pedir[i]=`echo $line | awk {'print $5'}`
+    rotime[i]=`echo $line | awk {'print $6'}`
+    echo -n "${pedir[i]} " >> ${prepFolder}/eddy/eddyIndex.txt
+    if [ ${bval[i]} -eq 0 ]; then
+	if [ ${pedir[i]} -eq 1 ]; then #LR
+	    LRvols[idxLR]=$i
+	    idxLR=$(($idxLR + 1))	
+	elif [ ${pedir[i]} -eq 2 ]; then #RL
+	    RLvols[idxRL]=$i
+	    idxRL=$(($idxRL + 1))
+	elif [ ${pedir[i]} -eq 3 ]; then #AP
+	    APvols[idxAP]=$i
+	    idxAP=$(($idxAP + 1))
+	elif [ ${pedir[i]} -eq 4 ]; then #PA
+	    PAvols[idxPA]=$i
+	    idxPA=$(($idxPA + 1))
+	fi
+    else
+	if [ ${pedir[i]} -eq 1 ]; then #LR
+	    no_LR=$(($no_LR + 1))
+	elif [ ${pedir[i]} -eq 2 ]; then #RL
+	    no_RL=$(($no_RL + 1))
+	elif [ ${pedir[i]} -eq 3 ]; then #AP
+	    no_AP=$(($no_AP + 1))
+	elif [ ${pedir[i]} -eq 4 ]; then #PA
+	    no_PA=$(($no_PA + 1))
+	fi
+	if [ ${bval[i]} -eq 400 ]; then
+	    idxb400=$(($idxb400+1))
+	elif [ ${bval[i]} -eq 1000 ]; then
+	    idxb1000=$(($idxb1000+1))
+	elif [ ${bval[i]} -eq 2600 ]; then
+	    idxb2600=$(($idxb2600+1))
+	fi
+    fi
+    i=$(($i + 1))
+    if [ $i -eq ${nVols} ]; then
+	break
+    fi
+done < ${acqProt}
+
+
+#============================================================================
+# Write json file for QC
+#============================================================================
+echo "{" > ${prepFolder}/dataImport.json
+
+echo "   \"no_B400_vols\": $idxb400," >> ${prepFolder}/dataImport.json
+echo "   \"no_B1000_vols\": $idxb1000," >> ${prepFolder}/dataImport.json
+echo "   \"no_B2600_vols\": $idxb2600," >> ${prepFolder}/dataImport.json
+
+echo "   \"no_LR_vols\": $no_LR," >> ${prepFolder}/dataImport.json
+echo "   \"no_RL_vols\": $no_RL," >> ${prepFolder}/dataImport.json
+echo "   \"no_AP_vols\": $no_AP," >> ${prepFolder}/dataImport.json
+echo "   \"no_PA_vols\": $no_PA" >> ${prepFolder}/dataImport.json
+
+echo "}" >> ${prepFolder}/dataImport.json
+
+
+#============================================================================
+# Write bvecs, bvals and eddy acquisition parameters file.
+#============================================================================
+echo "${bvec_x[@]}" > ${prepFolder}/tmpData/bvecs
+echo "${bvec_y[@]}" >> ${prepFolder}/tmpData/bvecs
+echo "${bvec_z[@]}" >> ${prepFolder}/tmpData/bvecs
+echo "${bval[@]}" > ${prepFolder}/bvals
+
+if [ $LRvols -ne -1 ]; then
+    echo -1 0 0 ${rotime[${LRvols[0]}]} > ${prepFolder}/eddy/acqparamsUnwarp.txt
+else
+    echo -1 0 0 0.05 > ${prepFolder}/eddy/acqparamsUnwarp.txt
+fi
+if [ $RLvols -ne -1 ]; then
+    echo 1 0 0 ${rotime[${RLvols[0]}]} >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+else
+    echo 1 0 0 0.05 >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+fi
+if [ $APvols -ne -1 ]; then
+    echo 0 -1 0 ${rotime[${APvols[0]}]} >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+else
+    echo 0 -1 0 0.05 >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+fi
+if [ $PAvols -ne -1 ]; then
+    echo 0 1 0 ${rotime[${PAvols[0]}]} >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+else
+    echo 0 1 0 0.05 >> ${prepFolder}/eddy/acqparamsUnwarp.txt
+fi
+
+#============================================================================
+# Reorient raw data and bvecs to standard orientations
+#============================================================================
+${FSLDIR}/bin/fslreorient2std ${dataFolder}/${dataFile} ${prepFolder}/tmpData/data
+${FSLDIR}/bin/fslreorient2std ${dataFolder}/${dataFile} > ${prepFolder}/tmpData/raw2std.mat
+
+echo 1 0 0 0 > ${prepFolder}/tmpData/flipZ.mat
+echo 0 1 0 0 >> ${prepFolder}/tmpData/flipZ.mat
+echo 0 0 -1 0 >> ${prepFolder}/tmpData/flipZ.mat
+echo 0 0 0 1 >> ${prepFolder}/tmpData/flipZ.mat
+
+${scriptsFolder}/utils/rotateBvecs.sh ${prepFolder}/tmpData/bvecs ${prepFolder}/tmpData/raw2std.mat ${prepFolder}/tmpData/bvecs2
+${scriptsFolder}/utils/rotateBvecs.sh ${prepFolder}/tmpData/bvecs2 ${prepFolder}/tmpData/flipZ.mat ${prepFolder}/bvecs
+
+#============================================================================
+# Check that in-plane matrix size is a multiple of 2 (for TOPUP)
+#============================================================================
+dimt1=`${FSLDIR}/bin/fslval ${prepFolder}/tmpData/data dim1`
+c1=$(($dimt1%2))
+if [ $c1 -ne 0 ]; then
+    ${FSLDIR}/bin/fslroi ${prepFolder}/tmpData/data ${prepFolder}/tmpData/tmp 0 1 0 -1 0 -1 0 -1
+    ${FSLDIR}/bin/fslmerge -x ${prepFolder}/tmpData/data ${prepFolder}/tmpData/data ${prepFolder}/tmpData/tmp
+fi
+dimt2=`${FSLDIR}/bin/fslval ${prepFolder}/tmpData/data dim2`
+c2=$(($dimt2%2))
+if [ $c2 -ne 0 ]; then
+    ${FSLDIR}/bin/fslroi ${prepFolder}/tmpData/data ${prepFolder}/tmpData/tmp 0 -1 0 1 0 -1 0 -1
+    ${FSLDIR}/bin/fslmerge -y ${prepFolder}/tmpData/data ${prepFolder}/tmpData/data ${prepFolder}/tmpData/tmp
+fi
+
+
+#============================================================================
+# Identify best b0s for every acquired PE direction
+#============================================================================
+echo "${LRvols[@]}" > ${prepFolder}/topup/b0Indices
+echo "${RLvols[@]}" >> ${prepFolder}/topup/b0Indices
+echo "${APvols[@]}" >> ${prepFolder}/topup/b0Indices
+echo "${PAvols[@]}" >> ${prepFolder}/topup/b0Indices
+
+if [ $LRvols -ne -1 ]; then 
+    tmp=$(printf ",%s" "${LRvols[@]}")
+    tmp=${tmp:1}
+    ${FSLDIR}/bin/fslselectvols -i ${prepFolder}/tmpData/data -o ${prepFolder}/topup/LR_B0s --vols=${tmp}
+    $scriptsFolder/utils/pickBestB0s.sh ${prepFolder}/topup 0 ${noB0s}
+fi
+if [ $RLvols -ne -1 ]; then 
+    tmp=$(printf ",%s" "${RLvols[@]}")
+    tmp=${tmp:1}
+    ${FSLDIR}/bin/fslselectvols -i ${prepFolder}/tmpData/data -o ${prepFolder}/topup/RL_B0s --vols=${tmp}
+    $scriptsFolder/utils/pickBestB0s.sh ${prepFolder}/topup 1 ${noB0s}
+fi
+if [ $APvols -ne -1 ]; then 
+    tmp=$(printf ",%s" "${APvols[@]}")
+    tmp=${tmp:1}
+    ${FSLDIR}/bin/fslselectvols -i ${prepFolder}/tmpData/data -o ${prepFolder}/topup/AP_B0s --vols=${tmp}
+    $scriptsFolder/utils/pickBestB0s.sh ${prepFolder}/topup 2 ${noB0s}
+fi
+if [ $PAvols -ne -1 ]; then 
+    tmp=$(printf ",%s" "${PAvols[@]}")
+    tmp=${tmp:1}
+    ${FSLDIR}/bin/fslselectvols -i ${prepFolder}/tmpData/data -o ${prepFolder}/topup/PA_B0s --vols=${tmp}
+    $scriptsFolder/utils/pickBestB0s.sh ${prepFolder}/topup 3 ${noB0s}
+fi
+
+
+#============================================================================
+# Sort b0s based on their scores, merge them in a file and write acqparams
+# for topup and reference scan for eddy.
+#============================================================================
+bestPE=(`cat ${prepFolder}/topup/idxBestB0s.txt | sort -k 3 -n | head -n 4 | awk '{print $1}'`)
+bestVol=(`cat ${prepFolder}/topup/idxBestB0s.txt | sort -k 3 -n | head -n 4 | awk '{print $2}'`)
+
+acqpPE=("-1 0 0" "1 0 0" "0 -1 0" "0 1 0")
+PE=("LR" "RL" "AP" "PA")
+count=0
+echo -n > ${prepFolder}/topup/acqparams.txt
+for i in "${bestPE[@]}" ; do
+    dimt4=`${FSLDIR}/bin/fslval ${prepFolder}/topup/"${PE[$i]}"_B0s.nii.gz dim4`
+    for j in $(seq 0 $((${dimt4}-1))) ; do 
+	echo "${acqpPE[$i]}" "${rotime[${bestVol[${count}]}]}" >> ${prepFolder}/topup/acqparams.txt
+    done
+    PE_B0s[$count]=${prepFolder}/topup/"${PE[$i]}"_B0s.nii.gz
+    count=$(($count+1))
+done
+echo ${PE_B0s[@]}
+${FSLDIR}/bin/fslmerge -t ${prepFolder}/topup/phase ${PE_B0s[@]}
+
+
+echo "${bestVol[0]}" > ${prepFolder}/eddy/ref_scan.txt
+
+
+echo -e "\n END: Importing files"
+

dHCP_neo_dMRI_runBPX.sh

+#!/bin/bash
+set -e
+echo -e "\n START: running BPX model 3..."
+
+
+diffFolder=$1
+
+
+#============================================================================
+# Run BPX model 3
+#============================================================================
+${FSLDIR}/bin/bedpostx ${diffFolder} -n 3 -b 3000 -model 3 --Rmean=0.3
+
+
+echo -e "\n END: runBPX"
+

dHCP_neo_dMRI_runEddy.sh

+#!/bin/bash
+set -e
+echo -e "\n START: runEddy"
+
+
+prepFolder=$1
+dataFile=$2
+
+topupFolder=${prepFolder}/topup
+eddyFolder=${prepFolder}/eddy
+
+ref_scan=`cat ${eddyFolder}/ref_scan.txt`
+
+${FSLDIR}/bin/eddy_cuda --imain=${dataFile} --mask=${topupFolder}/nodif_brain_mask.nii.gz --index=${eddyFolder}/eddyIndex.txt --bvals=${prepFolder}/bvals --bvecs=${prepFolder}/bvecs --acqp=${eddyFolder}/acqparamsUnwarp.txt --topup=${topupFolder}/topup_results --out=${eddyFolder}/eddy_corrected --very_verbose --niter=5 --fwhm=10,5,0,0,0 --s2v_niter=10 --mporder=8 --nvoxhp=5000 --slspec=${scriptsFolder}/slorder.txt --repol --ol_type=both --s2v_interp=trilinear --s2v_lambda=1 --ref_scan_no=${ref_scan} --data_is_shelled --cnr_maps --residuals --dont_mask_output
+
+
+#============================================================================
+# Run bet on average iout.
+#============================================================================
+echo "Running BET on the hifi b0"
+${FSLDIR}/bin/select_dwi_vols ${eddyFolder}/eddy_corrected ${prepFolder}/bvals ${eddyFolder}/hifib0 0 -m
+${FSLDIR}/bin/bet ${eddyFolder}/hifib0 ${eddyFolder}/nodif_brain -m -f 0.25 -R
+
+
+#================
+# Quality Control
+#================
+i=-1
+n_ol_b400=0
+n_ol_b1000=0
+n_ol_b2600=0
+n_ol_LR=0
+n_ol_RL=0
+n_ol_AP=0
+n_ol_PA=0
+bvals=($(head -n 1 ${prepFolder}/bvals))
+eddyIndex=($(head -n 1 ${eddyFolder}/eddyIndex.txt))
+dimt3=`${FSLDIR}/bin/fslval ${eddyFolder}/eddy_corrected.nii.gz dim3`
+dimt4=`${FSLDIR}/bin/fslval ${eddyFolder}/eddy_corrected.nii.gz dim4`
+
+# Compute outlier stats
+#   n_ol_sl: number of times slice n has been classified as an outlier
+#   n_ol_vol: number of outlier slices in each volume
+#   n_ol_b*: number of outlier slices for each b-value shell
+#   n_ol_*: number of outlier slices for each phase encode direction
+#   tot_ol: total number of outliers
+while read line
+do
+    if [ $i -ge 0 ]; then
+	#echo ${line}
+	tmp=(${line})
+	a=0
+	for ((ii=0; ii<$dimt3; ii++)); do
+	    a=$((${a}+${tmp[ii]}))
+	    n_ol_sl[ii]=$((${n_ol_sl[ii]}+${tmp[ii]}))
+	done
+	n_ol_vol[i]=$a
+	if [ ${bvals[i]} -eq 400 ]; then
+	    n_ol_b400=$((${n_ol_b400}+${a}))
+	elif [ ${bvals[i]} -eq 1000 ]; then
+	    n_ol_b1000=$((${n_ol_b1000}+${a}))
+	elif [ ${bvals[i]} -eq 2600 ]; then
+	    n_ol_b2600=$((${n_ol_b2600}+${a}))
+	fi
+	if [ ${eddyIndex[i]} -eq 1 ]; then
+	    n_ol_LR=$((${n_ol_LR}+${a}))
+	elif [ ${eddyIndex[i]} -eq 2 ]; then
+	    n_ol_RL=$((${n_ol_RL}+${a}))
+	elif [ ${eddyIndex[i]} -eq 3 ]; then
+	    n_ol_AP=$((${n_ol_AP}+${a}))
+	elif [ ${eddyIndex[i]} -eq 4 ]; then
+	    n_ol_PA=$((${n_ol_PA}+${a}))
+	fi
+    fi
+    i=$(($i + 1))
+done < ${eddyFolder}/eddy_corrected.eddy_outlier_map
+tot_ol=$((${n_ol_b400}+${n_ol_b1000}+${n_ol_b2600}))
+
+# Compute average subject motion
+#   m_abs: average absolute subject motion
+#   m_rel: average relative subject motion
+m_abs=0
+m_rel=0
+while read line
+do
+    # Read first column from EDDY output
+    val=`echo $line | awk {'print $1'}`
+    # To handle scientific notation, we need the following line
+    val=`echo ${val} | sed -e 's/[eE]+*/\\*10\\^/'`
+    m_abs=`echo "${m_abs} + ${val}" | bc -l`
+    # Read second column from EDDY output
+    val=`echo $line | awk {'print $2'}`
+    # To handle scientific notation, we need the following line
+    val=`echo ${val} | sed -e 's/[eE]+*/\\*10\\^/'`
+    m_rel=`echo "${m_rel} + ${val}" | bc -l`
+done < ${eddyFolder}/eddy_corrected.eddy_movement_rms
+m_abs=`echo "${m_abs} / ${dimt4}" | bc -l`
+m_rel=`echo "${m_rel} / ${dimt4}" | bc -l`
+
+# Write .json file
+echo "{" > ${eddyFolder}/eddy_corrected.json
+echo "   \"Tot_ol\": $tot_ol," >> ${eddyFolder}/eddy_corrected.json
+tmp=$(printf ", %s" "${n_ol_vol[@]}")
+tmp=${tmp:2}
+echo "   \"No_ol_volumes\": [$tmp]," >> ${eddyFolder}/eddy_corrected.json
+tmp=$(printf ", %s" "${n_ol_sl[@]}")
+tmp=${tmp:2}
+echo "   \"No_ol_slices\": [$tmp]," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_b400\": $n_ol_b400," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_b1000\": $n_ol_b1000," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_b2600\": $n_ol_b2600," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_LR\": $n_ol_LR," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_RL\": $n_ol_RL," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_AP\": $n_ol_AP," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"No_ol_PA\": $n_ol_PA," >> ${eddyFolder}/eddy_corrected.json
+echo "   \"Avg_motion\": $m_abs" >> ${eddyFolder}/eddy_corrected.json
+echo "}" >> ${eddyFolder}/eddy_corrected.json
+
+
+echo -e "\n END: runEddy"
+

dHCP_neo_dMRI_runPostProc.sh

+#!/bin/bash
+set -e
+echo -e "\n START: runPostProc"
+
+
+prepFolder=$1
+diffFolder=$2
+qcFlag=$3
+
+topupFolder=${prepFolder}/topup
+eddyFolder=${prepFolder}/eddy
+
+if [ ${qcFlag} -eq 1 ]; then
+    mkdir -p ${prepFolder}/QC
+fi
+mkdir -p ${diffFolder}
+
+#============================================================================
+# Remove negative intensity values (caused by spline interpolation) from 
+# pre-processed data. Copy bvals and (rotated) bvecs to the Diffusion folder.
+#============================================================================
+${FSLDIR}/bin/fslmaths ${eddyFolder}/data_sr -thr 0 ${diffFolder}/data
+rm ${eddyFolder}/data_sr.*
+cp ${prepFolder}/bvals ${diffFolder}/bvals
+cp ${eddyFolder}/eddy_corrected.eddy_rotated_bvecs ${diffFolder}/bvecs
+
+#============================================================================
+# Get the brain mask using BET, average shell data and attenuation profiles.
+# Fit diffusion tensor to each shell separately. If interested in qc, store
+# volumes and variances.
+#============================================================================
+uniqueBvals=(0 400 1000 2600)
+for b in "${uniqueBvals[@]}"; do
+    ${FSLDIR}/bin/select_dwi_vols ${diffFolder}/data ${diffFolder}/bvals ${diffFolder}/mean_b${b} ${b} -m
+    if [ ${qcFlag} -eq 1 ]; then
+	${FSLDIR}/bin/select_dwi_vols ${diffFolder}/data ${diffFolder}/bvals ${prepFolder}/QC/vols_b${b} ${b}
+	${FSLDIR}/bin/select_dwi_vols ${diffFolder}/data ${diffFolder}/bvals ${prepFolder}/QC/var_b${b} ${b} -v
+    fi
+    if [ ${b} -eq 0 ]; then
+	${FSLDIR}/bin/bet ${diffFolder}/mean_b${b} ${diffFolder}/nodif_brain -m -f 0.25 -R
+    else
+	echo "Multi-shell data: fitting DT to b=${b} shell..."
+	mkdir -p ${diffFolder}/dtifit_b${b}
+	${FSLDIR}/bin/select_dwi_vols ${diffFolder}/data ${diffFolder}/bvals ${diffFolder}/dtifit_b${b}/b${b} 0 -b ${b} -obv ${diffFolder}/bvecs 
+	${FSLDIR}/bin/dtifit -k ${diffFolder}/dtifit_b${b}/b${b} -o ${diffFolder}/dtifit_b${b}/dti -m ${diffFolder}/nodif_brain_mask -r ${diffFolder}/dtifit_b${b}/b${b}.bvec -b ${diffFolder}/dtifit_b${b}/b${b}.bval --sse --save_tensor
+	${FSLDIR}/bin/fslmaths ${diffFolder}/mean_b${b} -div ${diffFolder}/mean_b0 -mul ${diffFolder}/nodif_brain_mask ${diffFolder}/att_b${b}
+    fi
+    ${FSLDIR}/bin/fslmaths ${diffFolder}/mean_b${b} -mul ${diffFolder}/nodif_brain_mask ${diffFolder}/mean_b${b}
+done
+
+#============================================================================
+# Fit Kurtosis model.
+#============================================================================
+echo "Multi-shell data: fitting DK to all shells..."
+mkdir -p ${diffFolder}/dkifit
+${FSLDIR}/bin/dtifit -k ${diffFolder}/data -o ${diffFolder}/dkifit/dki -m ${diffFolder}/nodif_brain_mask -r ${diffFolder}/bvecs -b ${diffFolder}/bvals --sse --save_tensor --kurt --kurtdir
+
+
+#rm -R ${preprocdir}/tmpData
+
+
+echo -e "\n END: runPostProc"
+

dHCP_neo_dMRI_runTopup.sh

+#!/bin/bash
+
+set -e
+echo -e "\n Running topup..."
+
+
+topupDir=$1   # Folder where input files are and where output will be stored
+
+topupConfigFile=${FSLDIR}/etc/flirtsch/b02b0.cnf
+
+
+#============================================================================
+# Run topup on the selected b0 volumes.
+#============================================================================
+${FSLDIR}/bin/topup --imain=${topupDir}/phase --datain=${topupDir}/acqparams.txt --config=${topupConfigFile} --fout=${topupDir}/fieldmap --iout=${topupDir}/topup_b0s --out=${topupDir}/topup_results -v
+
+
+#============================================================================
+# Run bet on average iout.
+#============================================================================
+echo "Running BET on the hifi b0"
+${FSLDIR}/bin/fslmaths ${topupDir}/topup_b0s -Tmean ${topupDir}/topup_hifib0
+${FSLDIR}/bin/bet ${topupDir}/topup_hifib0 ${topupDir}/nodif_brain -m -f 0.25 -R
+
+
+echo -e "\n END: runTopup."
+

dHCP_neo_dMRI_setJobs.sh

+#!/bin/bash
+
+
+set -e
+echo -e "\n START: Setting up jobs for the dHCP neonatal dMRI data processing pipeline"
+
+
+if [ "$9" == "" ];then
+    echo "The script will queue all the jobs necessary to process dHCP neonatal dMRI data"
+    echo ""
+    echo "usage: $0 <data folder> <session folder> <data file> <connectome ID> <acquisition protocol> <readout time> <output folder> <age at scan> <age at birth> <no. sessions>"
+    echo ""
+    echo "       data folder: path where the session data is stored"
+    echo "       session folder: session folder name"
+    echo "       data file: raw data file name"
+    echo "       connectome ID: connectome ID number (CC...)"
+    echo "       acquisition protocol: name of the text file containing gradient orientations, b-values and phase encoding directions"
+    echo "       output folder: folder where results will be stored"
+    echo "       age at scan: in weeks (GA)"
+    echo "       age at birth: in weeks (GA)"
+    echo "       no. sessions: number of sessions"
+    echo ""
+    echo ""
+    exit 1
+fi
+
+dataFolder=$1          # Path to data folder
+sessionFolder=$2       # Session number
+dataFile=$3	       # FileName to avoid confusion...
+connID=$4              # Unique connectome ID
+acqProt=$5             # Acquisition protocol file
+outFolder=$6           # Path where the processed subjects will be stored
+ageScan=$7             # Age at scan (w GA)
+ageBirth=$8            # Age at birth (w GA)
+nSessions=$9           # Number of sessions
+
+noB0s=2                # Number of B0 volumes for each PE direction used to estimate distortions with TOPUP
+
+
+#============================================================================
+# Check for scan completeness
+#============================================================================
+dimt4=`${FSLDIR}/bin/fslval ${dataFolder}/${sessionFolder}/DWI/${dataFile} dim4`
+complete_check=${dimt4}
+usable_check=1
+if [ $dimt4 -lt 34 ]; then
+    echo "WARNING: The dataset is unusable as it does not contain enough B0 volumes"
+    SubjFolder=/vols/Data/baby/DMRI_pipeline_testing/unusable_"$ConnID"
+    mkdir -p ${SubjFolder}
+    usable_check=0
+    exit 1
+elif [ $dimt4 -lt 123 ]; then
+    echo "WARNING: The dataset is incomplete and does not contain enough B0 pairs for each PE direction"
+    noB0s=1
+    usable_check=1
+fi
+
+
+#============================================================================
+# Create directory structure and write ages
+#============================================================================
+subjOutFolder=${outFolder}/${connID}/${sessionFolder}
+
+prepFolder=${subjOutFolder}/PreProcessed
+anatFolder=${subjOutFolder}/T2w
+diffFolder=${subjOutFolder}/Diffusion
+
+mkdir -p ${prepFolder}/topup
+mkdir -p ${prepFolder}/eddy
+mkdir -p ${prepFolder}/tmpData
+mkdir -p ${anatFolder}
+mkdir -p ${diffFolder}
+
+echo `awk -v v="$ageScan" 'BEGIN{printf "%.0f", v}'` > ${subjOutFolder}/age
+echo `awk -v v="$ageBirth" 'BEGIN{printf "%.0f", v}'` > ${subjOutFolder}/birth
+
+
+#============================================================================
+# Store QC information
+#============================================================================
+echo "{" > ${subjOutFolder}/initQC.json
+echo "   \"Complete\": ${complete_check}," >> ${subjOutFolder}/initQC.json
+echo "   \"Usable\": ${usable_check}," >> ${subjOutFolder}/initQC.json
+echo "   \"nSessions\": ${nSessions}," >> ${subjOutFolder}/initQC.json
+echo "   \"birthAge\": ${ageBirth}," >> ${subjOutFolder}/initQC.json
+echo "   \"scanAge\": ${ageScan}" >> ${subjOutFolder}/initQC.json
+echo "}" >> ${subjOutFolder}/initQC.json
+
+
+#============================================================================
+# Prepare super-resolution commands
+#============================================================================
+${scriptsFolder}/superres/setup_superres.sh ${prepFolder}/eddy/eddy_corrected.nii.gz ${prepFolder}/eddy/nodif_brain_mask.nii.gz ${prepFolder}/eddy/sr_commands.txt ${dimt4}
+
+
+#============================================================================
+# Set main chain starting from last completed step
+#============================================================================
+if [ ! -e ${prepFolder}/eddy/eddy_corrected.nii.gz ]; then
+    
+    #============================================================================
+    # Import files and create initial structure
+    #============================================================================
+    importid=`${FSLDIR}/bin/fsl_sub -q short.q -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_importFiles.sh ${dataFolder}/${sessionFolder}/DWI ${dataFile} ${prepFolder} ${acqProt} ${dimt4} ${noB0s}`
+
+    #============================================================================
+    # Run TOPUP
+    #============================================================================
+    topupid=`${FSLDIR}/bin/fsl_sub -q short.q -j ${importid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runTopup.sh ${prepFolder}/topup`
+    
+    #============================================================================
+    # EDDY run with outlier detection and replacemetn, s2v and no masking of out-of-FOV voxels
+    #============================================================================
+    eddyid=`${FSLDIR}/bin/fsl_sub -q cuda.q -j ${topupid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runEddy.sh ${prepFolder} ${prepFolder}/tmpData/data`
+    
+    #============================================================================
+    # Super resolution for EDDY corrected data
+    #============================================================================
+    pre_srid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${eddyid} -l ${prepFolder}/logs ${scriptsFolder}/superres/prerun_superres.sh ${prepFolder}/eddy/eddy_corrected.nii.gz`
+
+    srid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${pre_srid} -l ${prepFolder}/logs -t ${prepFolder}/eddy/sr_commands.txt`
+    
+    post_srid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${srid} -l ${prepFolder}/logs ${scriptsFolder}/superres/postrun_superres.sh ${prepFolder}/eddy/eddy_corrected.nii.gz`
+
+    #============================================================================
+    # Run EDDY post processing steps and DT fit
+    #============================================================================
+    pprocid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${post_srid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runPostProc.sh ${prepFolder} ${diffFolder} 1`
+
+    #============================================================================
+    # Run BPX model 3
+    #============================================================================
+    bpxid=`${FSLDIR}/bin/fsl_sub -q cuda.q -j ${pprocid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runBPX.sh ${diffFolder}`
+
+    #============================================================================
+    # Coregister DWI with Structural T2 (native and template spaces)
+    #============================================================================
+    regid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${pprocid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runRegistration.sh ${anatFolder} ${subjOutFolder} ${t2Folder} ${segFolder} ${surfFolder} ${dofsFolder}`
+    
+    #============================================================================
+    # Generate PNGs for QC reports
+    #============================================================================
+    pngid=`${FSLDIR}/bin/fsl_sub -q short.q -j ${regid} -l ${prepFolder}/logs ${scriptsFolder}/utils/generateFigs.sh ${subjOutFolder}`
+    
+else
+
+    #============================================================================
+    # Run EDDY post processing steps
+    #============================================================================
+    pprocid=`${FSLDIR}/bin/fsl_sub -q cuda.q -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runPostProc.sh ${prepFolder} ${diffFolder} 1`
+    
+    #============================================================================
+    # Run BPX model 3
+    #============================================================================
+    bpxid=`${FSLDIR}/bin/fsl_sub -q cuda.q -j ${pprocid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runBPX.sh ${diffFolder}`
+
+    #============================================================================
+    # Coregister DWI with Structural T2 (native and template spaces)
+    #============================================================================
+    regid=`${FSLDIR}/bin/fsl_sub -q long.q -j ${pprocid} -l ${prepFolder}/logs ${scriptsFolder}/dHCP_neo_dMRI_runRegistration.sh ${anatFolder} ${subjOutFolder} ${t2Folder} ${segFolder} ${surfFolder} ${dofsFolder}`
+
+    #============================================================================
+    # Generate PNGs for QC reports
+    #============================================================================
+    pngid=`${FSLDIR}/bin/fsl_sub -q short.q -j ${regid} -l ${prepFolder}/logs ${scriptsFolder}/utils/generateFigs.sh ${subjOutFolder}`
+    
+fi
+
+echo -e "\n END: Setting up jobs for the dHCP neonatal dMRI data processing pipeline"

dHCP_neo_dMRI_setup.sh

+#!/bin/bash