Files/Structure for the new testing dataset

data/code/batch_list.txt

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+sub-01 0.75 0.01 run-01_scans

data/code/sub-01_run-01_scans.txt

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+sub-01_run-01_T2w axial
+sub-01_run-02_T2w coronal
+sub-01_run-03_T2w sagittal

data/code/superresolution_batch.sh

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+#!/bin/sh
+# usage:
+# sh generic_script_to_run_superresolution.sh /path/to/batch_list.txt
+
+# Get the directory where the script is stored,
+# which is supposed to be in the code folder of the dataset root directory)
+SCRIPT_DIR="$(dirname "$0")"
+
+#Get absolute path
+SCRIPT_DIR="$(readlink -f $SCRIPT_DIR)"
+
+DATASET_DIR="$(dirname "${SCRIPT_DIR}")"
+
+echo "Dataset directory : $DATASET_DIR"
+
+#from each line of the subject_parameters.txt given as input
+while read -r line
+  do
+  #Extract PATIENT, LAMBDA_TV and DELTA_T and the scan list sub-01_run-01_scans.txt
+	set -- $line
+	PATIENT=$1
+	LAMBDA_TV=$2
+  DELTA_T=$3
+  SCANS_LIST="${PATIENT}_${4}.txt"
+
+  echo "> Process subject ${PATIENT} with lambda_tv = ${LAMBDA_TV} and delta_t = ${DELTA_T}"
+
+  PATIENT_DIR="$DATASET_DIR/${PATIENT}"
+  echo "  ... Subject directory : ${PATIENT_DIR}"
+
+  # Create the output directory for results (if not existing). 
+  # run-XX is used to identify different list of scans:
+  # sub-01_run-01_scans.txt, sub-01_run-02_scans.txt, ..., sub-01_run-XX_scans.txt
+  # here I am just using sub-01_run-01_scans.txt but you can think as I am looping over 
+  # the different calls while reading the batch_list.txt file, 
+  # you could  similarly loop over different list of scans.
+  # The final superesolution is saved in derivatives/mialsrtk_tv-${LAMBDA_TV}_dt-${DELTA_T}_run-01/$PATIENT/anat folder
+  # All intermediate outputs are saved in a tmp folder (see below). 
+
+  RESULTS="derivatives/mialsrtk_tv-${LAMBDA_TV}_dt-${DELTA_T}_run-01/$PATIENT"
+  echo "  ... Reconstruction tmp directory: ${DATASET_DIR}/${RESULTS}"
+  if [ ! -d "${DATASET_DIR}/${RESULTS}" ]; then
+    mkdir -p "${DATASET_DIR}/${RESULTS}";
+    echo "    * Folder ${DATASET_DIR}/${RESULTS} created"
+  fi
+  if [ ! -d "${DATASET_DIR}/${RESULTS}/tmp" ]; then
+    mkdir -p "${DATASET_DIR}/${RESULTS}/tmp";
+    echo "    * Folder ${DATASET_DIR}/${RESULTS}/tmp created"
+  fi
+  if [ ! -d "${DATASET_DIR}/${RESULTS}/anat" ]; then
+    mkdir -p "${DATASET_DIR}/${RESULTS}/anat";
+    echo "    * Folder ${DATASET_DIR}/${RESULTS}/anat created"
+  fi
+
+  PATIENT_MASK_DIR="derivatives/manual_masks/$PATIENT"
+
+
+  # Run the super-resolution pipeline
+
+  docker run --rm -u $(id -u):$(id -g) \
+              -v $DATASET_DIR:/fetaldata \
+              --entrypoint /fetaldata/code/superresolution_pipeline.sh \
+              --env PATIENT="$PATIENT" \
+              --env DELTA_T="$DELTA_T" \
+              --env LAMBDA_TV="$LAMBDA_TV "\
+              --env PATIENT_DIR="/fetaldata/${PATIENT}" \
+              --env PATIENT_MASK_DIR="/fetaldata/${PATIENT_MASK_DIR}/anat" \
+              --env RESULTS="/fetaldata/${RESULTS}/tmp" \
+              -t sebastientourbier/mialsuperresolutiontoolkit:v1.1.0 \
+              "/fetaldata/code/${SCANS_LIST}"
+
+done < "$1"

data/code/superresolution_pipeline.sh

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+#!/bin/sh
+#! Script: Brain image reconstruction / Brain superresolution image using BTK
+# Run with log saved: sh reconstruction.sh > reconstruction_original_images.log 
+#Tune the number of cores used by the OpenMP library for multi-threading purposes
+export OMP_NUM_THREADS=$(grep -c ^processor /proc/cpuinfo 2>/dev/null || sysctl -n hw.ncpu)   
+
+echo 
+echo "-----------------------------------------------"
+echo
+
+echo "Starting superresolution pipeline for patient $PATIENT "
+
+echo 
+echo "-----------------------------------------------"
+echo
+
+#LAMBDA_TV=0.25       #0.75
+#DELTA_T=0.1
+LOOPS=10
+RAD_DILATION=1
+START_ITER=1
+MAX_ITER=1
+
+
+echo
+echo "Automated brain localization and extraction parameters"
+echo
+echo "Type of brain mask : ${maskType}"
+echo
+echo "Super-resolution parameters"
+echo
+echo "LAMBDA_TV : ${LAMBDA_TV}"
+echo "DELTA_T : ${DELTA_T}"
+echo "LOOPS : ${LOOPS}"
+echo
+echo "Brain mask refinement parameters"
+echo
+echo "Number of loops : ${DELTA_T}"
+echo "Morphological dilation radius : ${RAD_DILATION}"
+echo 
+echo "-----------------------------------------------"
+echo
+
+echo "Initialization..."
+
+START1=$(date +%s)
+
+echo 
+echo "-----------------------------------------------"
+echo
+
+echo "OMP # of cores set to ${OMP_NUM_THREADS}!"
+echo
+
+#export BIN_DIR="/usr/local/bin"
+printf "BIN_DIR=${BIN_DIR} \n"
+
+SCANS="${1}"
+echo "List of scans : $SCANS"
+
+
+echo "Everything set!"
+echo 
+echo "-----------------------------------------------"
+echo
+
+echo 
+echo "-----------------------------------------------"
+echo
+echo "Should do brain localization and extraction here, but need to make a selection of the best scans with the best brain masks before reconstruction."
+echo 
+echo "-----------------------------------------------"
+echo
+
+
+VOLS=0
+while read -r line
+do
+	VOLS=$((VOLS+1))
+done < "$SCANS"
+
+echo 
+echo "-----------------------------------------------"
+echo
+echo "Number of scans : ${VOLS}"
+echo 
+echo "-----------------------------------------------"
+echo
+
+##Iteration of motion estimation / reconstruction / brain mask refinement
+ITER="${START_ITER}"
+#for (( ITER=$START_ITER; ITER<=$MAX_ITER; ITER++ ))
+while [ "$ITER" -le "$MAX_ITER" ]
+do
+	echo "Performing iteration # ${ITER}"
+
+	cmdIntensity="mialsrtkIntensityStandardization"
+	cmdIntensityNLM="mialsrtkIntensityStandardization"
+	cmdHistogramNormalization="python ${BIN_DIR}/mialsrtkHistogramNormalization.py"
+	cmdHistogramNormalizationNLM="python ${BIN_DIR}/mialsrtkHistogramNormalization.py"
+
+	if [ "$ITER" -eq "1" ];
+	then
+
+		while read -r line
+		do
+			set -- $line
+			stack=$1
+			orientation=$2
+
+			echo "Process stack $stack with $orientation orientation..."
+
+		    #Reorient the image
+			mialsrtkOrientImage -i ${PATIENT_DIR}/${stack}.nii.gz -o $RESULTS/${stack}_reo_iteration_${ITER}.nii.gz -O "$orientation"
+			mialsrtkOrientImage -i ${PATIENT_MASK_DIR}/${stack}_desc-brain_mask.nii.gz -o $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -O "$orientation"
+
+			#denoising on reoriented images
+			weight="0.1"
+			btkNLMDenoising -i "$RESULTS/${stack}_reo_iteration_${ITER}.nii.gz" -o "$RESULTS/${stack}_nlm_reo_iteration_${ITER}.nii.gz" -b $weight
+
+			#Make slice intensities uniform in the stack
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_nlm_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_uni_reo_iteration_${ITER}.nii.gz"
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_uni_reo_iteration_${ITER}.nii.gz"
+
+			#bias field correction slice by slice
+			mialsrtkSliceBySliceN4BiasFieldCorrection "$RESULTS/${stack}_nlm_uni_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_n4bias.nii.gz"
+			mialsrtkSliceBySliceCorrectBiasField "$RESULTS/${stack}_uni_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_n4bias.nii.gz" "$RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+
+			#Intensity rescaling cmd preparation
+			cmdIntensityNLM="$cmdIntensityNLM -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			cmdIntensity="$cmdIntensity -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			cmdHistogramNormalization="$cmdHistogramNormalization -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz -m  $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+			cmdHistogramNormalizationNLM="$cmdHistogramNormalization -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz -m  $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+
+		done < "$SCANS"
+
+		echo "$cmdIntensity"
+
+	else
+
+		while read -r line
+		do
+			set -- $line
+			stack=$1
+
+			#Make slice intensities uniform in the stack
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_nlm_reo_iteration_1.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_nlm_uni_reo_iteration_${ITER}.nii.gz"
+			mialsrtkCorrectSliceIntensity "$RESULTS/${stack}_reo_iteration_1.nii.gz" "$RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz" "$RESULTS/${stack}_uni_reo_iteration_${ITER}.nii.gz"
+
+			cmdCorrectBiasField="mialsrtkCorrectBiasFieldWithMotionApplied -i $RESULTS/${stack}_nlm_uni_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField --input-bias-field $RESULTS/SRTV_${PATIENT}_${VOLS}V_lambda_${LAMBDA_TV}_deltat_${DELTA_T}_loops_${LOOPS}_rad${RAD_DILATION}_it${ITER}_gbcorrfield.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField --output-bias-field $RESULTS/${stack}_nlm_n4bias_iteration_${ITER}.nii.gz" 
+			cmdCorrectBiasField="$cmdCorrectBiasField -t $RESULTS/${stack}_transform_${VOLS}V_${LAST_ITER}.txt"
+			eval "$cmdCorrectBiasField"
+
+			cmdCorrectBiasField="mialsrtkCorrectBiasFieldWithMotionApplied -i $RESULTS/${stack}_uni_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField --input-bias-field $RESULTS/SRTV_${PATIENT}_${VOLS}V_lambda_${LAMBDA_TV}_deltat_${DELTA_T}_loops_${LOOPS}_rad${RAD_DILATION}_it${ITER}_gbcorrfield.nii.gz"
+			cmdCorrectBiasField="$cmdCorrectBiasField --output-bias-field $RESULTS/${stack}_n4bias_iteration_${ITER}.nii.gz" 
+			cmdCorrectBiasField="$cmdCorrectBiasField -t $RESULTS/${stack}_transform_${VOLS}V_${LAST_ITER}.txt"
+			eval "$cmdCorrectBiasField"
+
+			cmdIntensityNLM="$cmdIntensityNLM -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+			cmdIntensity="$cmdIntensity -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz"
+
+			cmdHistogramNormalization="$cmdHistogramNormalization -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}.nii.gz -m  $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+			cmdHistogramNormalizationNLM="$cmdHistogramNormalizationNLM -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}.nii.gz -m  $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+
+		done < "$SCANS"
+
+	fi
+
+
+	#Intensity rescaling
+	eval "$cmdIntensityNLM"
+	eval "$cmdIntensity"
+
+	#histogram normalization - need to change the brain mask name expected according to the one used (full auto/localization and rigid extraction/localization only/manual)
+	eval "$cmdHistogramNormalization"
+	eval "$cmdHistogramNormalizationNLM"
+
+	cmdIntensity="mialsrtkIntensityStandardization"
+	cmdIntensityNLM="mialsrtkIntensityStandardization"
+	while read -r line
+	do
+		set -- $line
+		stack=$1
+		#Intensity rescaling cmd preparation
+		cmdIntensityNLM="$cmdIntensityNLM -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz -o $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+		cmdIntensity="$cmdIntensity -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz -o $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+	done < "$SCANS"
+
+	#Intensity rescaling
+	eval "$cmdIntensityNLM"
+	eval "$cmdIntensity"
+
+	echo "Initialize the super-resolution image using initial masks - Iteration ${ITER}..."
+
+	cmdImageRECON="mialsrtkImageReconstruction --mask"
+	cmdSuperResolution="mialsrtkTVSuperResolution"
+	#cmdRobustSuperResolution="$MIALSRTK_APPLICATIONS/mialsrtkRobustTVSuperResolutionWithGMM"
+
+	#Preparation for (1) motion estimation and SDI reconstruction and (2) super-resolution reconstruction
+	while read -r line
+	do
+		set -- $line
+		stack=$1
+		mialsrtkMaskImage -i "$RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz" -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -o "$RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+
+		cmdImageRECON="$cmdImageRECON -i $RESULTS/${stack}_nlm_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+		cmdImageRECON="$cmdImageRECON -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
+		cmdImageRECON="$cmdImageRECON -t $RESULTS/${stack}_transform_${VOLS}V_${ITER}.txt"
+
+		cmdSuperResolution="$cmdSuperResolution -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+		cmdSuperResolution="$cmdSuperResolution -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
+		cmdSuperResolution="$cmdSuperResolution -t $RESULTS/${stack}_transform_${VOLS}V_${ITER}.txt"
+		#cmdRobustSuperResolution="$cmdRobustSuperResolution -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz -t $RESULTS/${stack}_transform_${VOLS}V_${ITER}.txt"
+	done < "$SCANS"
+
+	#Run motion estimation and SDI reconstruction
+	echo "Run motion estimation and scattered data interpolation - Iteration ${ITER}..."
+
+	cmdImageRECON="$cmdImageRECON -o $RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz"
+	eval "$cmdImageRECON"
+
+	echo "Done"
+	echo
+	echo "##########################################################################################################################"
+	echo
+
+	#Brain image super-reconstruction
+	echo "Reconstruct the super-resolution image with initial brain masks- Iteration ${ITER}..."
+
+	cmdSuperResolution="$cmdSuperResolution -o $RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz" 
+	cmdSuperResolution="$cmdSuperResolution -r $RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz" 
+	cmdSuperResolution="$cmdSuperResolution --bregman-loop 1 --loop ${LOOPS} --iter 50 --step-scale 10 --gamma 10 --deltat ${DELTA_T}" 
+	cmdSuperResolution="$cmdSuperResolution --lambda ${LAMBDA_TV} --inner-thresh 0.00001 --outer-thresh 0.000001"
+	echo "CMD: $cmdSuperResolution"
+	eval "$cmdSuperResolution"
+
+	echo "Done"
+	echo
+
+	#up="1.0"
+	#cmdRobustSuperResolution="$cmdRobustSuperResolution -o $RESULTS/RobustSRTV_${PATIENT}_${VOLS}V_NoNLM_bcorr_norm_lambda_${LAMBDA_TV}_deltat_${DELTA_T}_loops_${LOOPS}_it${ITER}_rad${RAD_DILATION}_up${up}.nii.gz -r $RESULTS/SDI_${PATIENT}_${VOLS}V_nlm_bcorr_norm_it${ITER}_rad${RAD_DILATION}.nii.gz --bregman-loop 1 --loop ${LOOPS} --iter 50 --step-scale 10 --gamma 10 --lambda ${LAMBDA_TV} --deltat ${DELTA_T} --inner-thresh 0.00001 --outer-thresh 0.000001 --use-robust --huber-mode 2 --upscaling-factor $up"
+	#eval "$cmdRobustSuperResolution"
+
+	NEXT_ITER=${ITER}
+	NEXT_ITER=$((NEXT_ITER+1))
+
+	echo "##########################################################################################################################"
+	echo
+
+	echo "Refine the mask of the HR image for next iteration (${NEXT_ITER})..."
+
+	echo
+	echo "##########################################################################################################################"
+	echo
+
+	#Preparation for brain mask refinement
+	cmdRefineMasks="mialsrtkRefineHRMaskByIntersection --use-staple --radius-dilation ${RAD_DILATION}"
+	while read -r line
+	do
+		set -- $line
+		stack=$1
+		cmdRefineMasks="$cmdRefineMasks -i $RESULTS/${stack}_uni_bcorr_reo_iteration_${ITER}_histnorm.nii.gz"
+		cmdRefineMasks="$cmdRefineMasks -m $RESULTS/${stack}_desc-brain_mask_reo_iteration_${ITER}.nii.gz"
+		cmdRefineMasks="$cmdRefineMasks -t $RESULTS/${stack}_transform_${VOLS}V_${ITER}.txt"
+		cmdRefineMasks="$cmdRefineMasks -O $RESULTS/${stack}_desc-brain_mask_reo_iteration_${NEXT_ITER}.nii.gz"
+	done < "$SCANS"
+
+	#Brain mask refinement
+
+	cmdRefineMasks="$cmdRefineMasks -o $RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_brain_mask.nii.gz -r $RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz"
+	eval "$cmdRefineMasks"
+
+	#Bias field refinement
+	mialsrtkN4BiasFieldCorrection "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz" "$RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_brain_mask.nii.gz" "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_gbcorr.nii.gz" "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_gbcorrfield.nii.gz"
+
+	#Brain masking of the reconstructed image
+
+	mialsrtkMaskImage -i "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}.nii.gz" -m "$RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_brain_mask.nii.gz" -o $RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${ITER}_masked.nii.gz
+
+	echo
+	echo "##########################################################################################################################"
+	echo
+
+	LAST_ITER="$ITER"
+	ITER=$((ITER+1))
+
+done
+
+FINAL_OUTPUT_DIR="$(dirname "$RESULTS")/anat"
+echo "Copy final outputs to ${FINAL_OUTPUT_DIR}"
+cp "$RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}.nii.gz" "${FINAL_OUTPUT_DIR}/${PATIENT}_rec-SDI_T2w.nii.gz"
+cp "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}.nii.gz" "${FINAL_OUTPUT_DIR}/${PATIENT}_rec-SR_T2w.nii.gz"
+cp "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}_masked.nii.gz" "${FINAL_OUTPUT_DIR}/${PATIENT}_desc-masked_rec-SR_T2w.nii.gz"
+
+echo
+echo "##########################################################################################################################"
+echo
+
+END1=$(date +%s)
+
+DIFF1=$(( $END1 - $START1 ))
+
+echo "Done. It took $DIFF1 seconds for reconstruction, after $MAX_ITER refinement loops, using ${VOLS} volumes."
+echo 
+echo "-----------------------------------------------"
+echo