SAMPLE DATA: Removed files and updated BIDS dataset

data/code/batch_list.txt

@@ -1 +1 @@
-sub-01 0.75 0.01 run-01_scans
+sub-01 ses-01 0.75 0.01 

data/code/superresolution_batch.sh

@@ -1,6 +1,10 @@
 #!/bin/sh
 # usage:
-# sh generic_script_to_run_superresolution.sh /path/to/batch_list.txt
+# sh superresolution_batch.sh /path/to/batch_list.txt v1.0.0
+# 
+# Author: Sebastien Tourbier
+# 
+###################################################################
 
 # Get the directory where the script is stored,
 # which is supposed to be in the code folder of the dataset root directory)
@@ -13,31 +17,55 @@ DATASET_DIR="$(dirname "${SCRIPT_DIR}")"
 
 echo "Dataset directory : $DATASET_DIR"
 
+VERSION_TAG=$2
+
 #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
+  #Extract PATIENT, LAMBDA_TV and DELTA_T and the scan list sub-01_ses-01_scans.txt
 	set -- $line
 	PATIENT=$1
-	LAMBDA_TV=$2
-  DELTA_T=$3
-  SCANS_LIST="${PATIENT}_${4}.txt"
+	LAMBDA_TV=$3
+  DELTA_T=$4
+  RECON_SESSION=$2
+  SCANS_LIST="${PATIENT}_${RECON_SESSION}_scans.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}"
 
+  # Get the number of scans in the list
+  # Can be used to differentiate output folders
+  # i.e. line RESULTS="derivatives/mialsrtk/$PATIENT/${RECON_SESSION}" would become
+  # RESULTS="derivatives/mialsrtk_scans-${VOLS}/$PATIENT/${RECON_SESSION}"
+
+  VOLS=0
+  while read -r line
+  do
+    VOLS=$((VOLS+1))
+  done < "${DATASET_DIR}/code/${SCANS_LIST}"
+
+  echo "  ... Number of scans : ${VOLS}"
+  echo
+
   # Create the output directory for results (if not existing). 
   # run-XX is used to identify different list of scans:
-  # sub-01_run-01_scans.txt, sub-01_run-02_scans.txt, ..., sub-01_run-XX_scans.txt
-  # here I am just using sub-01_run-01_scans.txt but you can think as I am looping over 
-  # the different calls while reading the batch_list.txt file, 
-  # you could  similarly loop over different list of scans.
-  # The final superesolution is saved in derivatives/mialsrtk_tv-${LAMBDA_TV}_dt-${DELTA_T}_run-01/$PATIENT/anat folder
+  # sub-01_ses-01_scans.txt, sub-01_ses-02_scans.txt, ..., sub-01_ses-XX_scans.txt
+  # The final superesolution is saved in derivatives/mialsrtk/$PATIENT/ses-XX/anat folder
   # All intermediate outputs are saved in a tmp folder (see below). 
+
+  if [ ! -d "${DATASET_DIR}/derivatives/mialsrtk" ]; then
+    mkdir -p "${DATASET_DIR}/derivatives/mialsrtk";
+    echo "    * Folder ${DATASET_DIR}/derivatives/mialsrtk created"
+  fi
+
+  if [ ! -f "${DATASET_DIR}/derivatives/mialsrtk/dataset_description.json" ];
+  then
+    sh ${DATASET_DIR}/code/create_dataset_description_json.sh "${DATASET_DIR}/derivatives/mialsrtk/dataset_description.json" "$VERSION_TAG"
+  fi
 
-  RESULTS="derivatives/mialsrtk_tv-${LAMBDA_TV}_dt-${DELTA_T}_run-01/$PATIENT"
+  RESULTS="derivatives/mialsrtk/$PATIENT/${RECON_SESSION}"
   echo "  ... Reconstruction tmp directory: ${DATASET_DIR}/${RESULTS}"
   if [ ! -d "${DATASET_DIR}/${RESULTS}" ]; then
     mkdir -p "${DATASET_DIR}/${RESULTS}";
@@ -51,6 +79,10 @@ while read -r line
     mkdir -p "${DATASET_DIR}/${RESULTS}/anat";
     echo "    * Folder ${DATASET_DIR}/${RESULTS}/anat created"
   fi
+  if [ ! -d "${DATASET_DIR}/${RESULTS}/xfm" ]; then
+    mkdir -p "${DATASET_DIR}/${RESULTS}/xfm";
+    echo "    * Folder ${DATASET_DIR}/${RESULTS}/xfm created"
+  fi
 
   PATIENT_MASK_DIR="derivatives/manual_masks/$PATIENT"
 
@@ -65,8 +97,8 @@ while read -r line
               --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 \
+              --env RESULTS="/fetaldata/${RESULTS}" \
+              -t sebastientourbier/mialsuperresolutiontoolkit:"$VERSION_TAG" \
               "/fetaldata/code/${SCANS_LIST}"
 
 

data/code/superresolution_pipeline.sh

@@ -1,9 +1,20 @@
 #!/bin/sh
-#! Script: Brain image reconstruction / Brain superresolution image using BTK
-# Run with log saved: sh reconstruction.sh > reconstruction_original_images.log 
+#
+# Script: Superresolution pipeline for fetal brain MRI
+#
+# Usage: Run with log saved: sh superresolution_pipeline.sh list_of_scans.txt > reconstruction_original_images.log 
+# 
+# Author: Sebastien Tourbier
+# 
+########################################################################################################################
+
 #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)   
 
+ANAT_DIR=$RESULTS/anat
+XFM_DIR=$RESULTS/xfm
+RESULTS=$RESULTS/tmp
+
 echo 
 echo "-----------------------------------------------"
 echo
@@ -295,12 +306,62 @@ do
 	ITER=$((ITER+1))
 
 done
+LAST_ITER=1
+
+
+# Extract absolute path of the folder containing the scripts (i.e. /fetaldata/code)
+CODE_DIR="$(dirname "$0")"
+CODE_DIR="$(readlink -f $CODE_DIR)"
+
+echo "Dataset code directory: ${CODE_DIR}"
+
+# Move the preprocessed input scans to anat and their associated slice-to-volume transform and 
+# create their respective json file (BIDS Common Derivatives RC1)
+
+SOURCES=""
+while read -r line
+do
+	set -- $line
+	stack=$1
+
+	# Copy and rename the transform and the image
+	cp "$RESULTS/${stack}_transform_${VOLS}V_${LAST_ITER}.txt" "${XFM_DIR}/${stack}_from-orig_to-SDI_mode-image_xfm.txt"
+	cp "$RESULTS/${stack}_uni_bcorr_reo_iteration_${LAST_ITER}_histnorm.nii.gz" "${ANAT_DIR}/${stack}_preproc.nii.gz"
+
+	# Create the BIDS json sidecar
+	sh ${CODE_DIR}/create_scan_preproc_json.sh "${ANAT_DIR}/${stack}_preproc.json" "${PATIENT_DIR}/${stack}.nii.gz" 
+
+	SOURCES="${SOURCES} \"${ANAT_DIR}/${stack}_preproc.nii.gz\", \"${XFM_DIR}/${stack}_from-orig_to-SDI_mode-image_xfm.txt\" ,"
+
+done < "$SCANS"
 
-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}_rec-SR_desc-masked_T2w.nii.gz"
+# Move the reconstructed images to anat and create the json file (BIDS Common Derivatives RC1)
+
+ANAT_DIR="$(dirname "$RESULTS")/anat"
+echo "Copy final outputs to ${ANAT_DIR}"
+cp "$RESULTS/SDI_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}.nii.gz" "${ANAT_DIR}/${PATIENT}_rec-SDI_T2w.nii.gz"
+cp "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}.nii.gz" "${ANAT_DIR}/${PATIENT}_rec-SR_T2w.nii.gz"
+cp "$RESULTS/SRTV_${PATIENT}_${VOLS}V_rad${RAD_DILATION}_it${LAST_ITER}_masked.nii.gz" "${ANAT_DIR}/${PATIENT}_rec-SR_desc-masked_T2w.nii.gz"
+
+
+# Create the json file for the super-resolution images
+OUTPUT_JSON="${ANAT_DIR}/${PATIENT}_rec-SR.json"
+(
+cat <<EOF
+{
+	"Description": "Isotropic high-resolution image reconstructed using the Total-Variation Super-Resolution algorithm provided by MIALSRTK",
+    "Sources": [${SOURCES}],
+    "CustomMetaData": {
+    	"Number of scans used":   $VOLS,
+		"TV regularization weight lambda": ${LAMBDA_TV},
+		"Optimization time step":   ${DELTA_T},
+		"Primal/dual loops": $LOOPS,
+		"Number of pipeline iterations" : ${LAST_ITER}
+	}
+}
+
+EOF
+) > $OUTPUT_JSON
 
 echo
 echo "##########################################################################################################################"