Update the script to SCT v7.2

etc/config_process_data_dcm-zurich.json

@@ -1,7 +1,7 @@
 {
-  "path_data"   : "/home/GRAMES.POLYMTL.CA/p118175/extrassd1/janvalosek/data/dcm-zurich",
-  "path_output" : "/home/GRAMES.POLYMTL.CA/p118175/extrassd1/janvalosek/dcm-zurich_2023-05-17_persex",
-  "script"      : "/home/GRAMES.POLYMTL.CA/p118175/code/dcm_metric_normalization/scripts/process_data_dcm-zurich.sh",
+  "path_data"   : "/Users/kahina/NeuroPoly/data/dcm-zurich",
+  "path_output" : "/Users/kahina/NeuroPoly/results/first_tests_sept25",
+  "script"      : "/Users/kahina/NeuroPoly/scr/dcm-metric-normalization/scripts/process_data_dcm-zurich.sh",
   "exclude_list"     : ["sub-817811", "sub-834907", "sub-842197", "sub-294305", "sub-796358", "sub-561017", "sub-250791", "sub-895299"],
-  "jobs"        : 32
+  "jobs"        : 4
 }

scripts/process_data_dcm-zurich.sh

@@ -41,18 +41,18 @@ segment_if_does_not_exist() {
   local contrast="$2"
   # Update global variable with segmentation file name
   FILESEG="${file}_label-SC_mask"
-  # TODO - change to FILESEG="${file}_label-SC_seg", once https://github.com/neuropoly/data-management/issues/225 is done
-  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILESEG}-manual.nii.gz"
+  # Getting the path for manual segmentation for each session
+  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${FILESEG}-manual.nii.gz"
   echo
   echo "Looking for manual segmentation: $FILESEGMANUAL"
   if [[ -e $FILESEGMANUAL ]]; then
     echo "Found! Using manual segmentation."
     rsync -avzh $FILESEGMANUAL ${FILESEG}.nii.gz
-    sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
+    sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
   else
     echo "Not found. Proceeding with automatic segmentation."
     # Segment spinal cord
-    sct_deepseg_sc -i ${file}.nii.gz -o ${FILESEG}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}
+    sct_deepseg spinalcord -i ${file}.nii.gz -o ${FILESEG}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
   fi
 }
 
@@ -64,25 +64,99 @@ label_if_does_not_exist(){
   local contrast="$3"
   # Update global variable with segmentation file name
   FILELABEL="${file}_labels"
-  # TODO - change to FILELABEL="${file}_label-disc", once https://github.com/neuropoly/data-management/issues/225 is done
-  FILELABELMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILELABEL}-manual.nii.gz"
+  FILELABELMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${FILELABEL}-manual.nii.gz"
   echo "Looking for manual disc labels: $FILELABELMANUAL"
   if [[ -e $FILELABELMANUAL ]]; then
     echo "Found! Using manual disc labels."
     rsync -avzh $FILELABELMANUAL ${FILELABEL}.nii.gz
     # Generate labeled segmentation from manual disc labels
-    sct_label_vertebrae -i ${file}.nii.gz -s ${file_seg}.nii.gz -discfile ${FILELABEL}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}
+    sct_label_vertebrae -i ${file}.nii.gz -s ${file_seg}.nii.gz -discfile ${FILELABEL}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
   else
     echo "Not found. Proceeding with automatic labeling."
     # Generate labeled segmentation automatically (no manual disc labels provided)
-    sct_label_vertebrae -i ${file}.nii.gz -s ${file_seg}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}
+    sct_label_vertebrae -i ${file}.nii.gz -s ${file_seg}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
   fi
   # Generate QC to access disc labels created by sct_label_vertebrae
-  sct_qc -i ${file}.nii.gz -s ${file_seg}_labeled_discs.nii.gz -p sct_label_utils -qc ${PATH_QC} -qc-subject ${SUBJECT}
+  sct_qc -i ${file}.nii.gz -s ${file_seg}_labeled_discs.nii.gz -p sct_label_utils -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
+}
+
+# Check if manual canal segmentation file already exists. If it does, copy it locally.
+# If it doesn't, perform automatic canal segmentation
+segment_canal_if_does_not_exist() {
+  local file="$1"
+  local contrast="$2"
+  # Update global variable with segmentation file name 
+  FILESEG="${file}_label-canal_seg"
+  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${FILESEG}.nii.gz"
+  echo
+  echo "Looking for manual canal segmentation: $FILESEGMANUAL"
+  if [[ -e $FILESEGMANUAL ]]; then
+    echo "Found! Using manual canal segmentation."
+    rsync -avzh $FILESEGMANUAL ${FILESEG}.nii.gz
+    sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
+  else
+    echo "Not found. Proceeding with automatic segmentation."
+    # Segment canal
+    sct_deepseg sc_canal_t2 -i ${file}.nii.gz -o ${FILESEG}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
+  fi
+}
+
+# Check if manual lesion segmentation file already exists. If it does, copy it locally.
+# If it doesn't, perform automatic lesion segmentation
+segment_lesion_if_does_not_exist() {
+  local file="$1"
+  local contrast="$2"
+  # Update global variable with segmentation file name 
+  FILESEG="${file}"
+  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${file}_label-lesion_seg.nii.gz"
+  echo
+  echo "Looking for manual lesion segmentation: $FILESEGMANUAL"
+  if [[ -e $FILESEGMANUAL ]]; then
+    echo "Found! Using manual lesion segmentation."
+    rsync -avzh $FILESEGMANUAL ${file}_lesion_seg.nii.gz
+    sct_qc -i ${file}.nii.gz -s ${file}_lesion_seg.nii.gz -p sct_deepseg_lesion -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
+  else
+    echo "Not found. Proceeding with automatic segmentation."
+    # Segment lesions
+    sct_deepseg lesion_sci_t2 -i ${file}.nii.gz -o ${file}.nii.gz -c ${contrast} -qc ${PATH_QC} -qc-subject ${SUBJECT}_${SESSION}
+  fi
 }
 
 # Retrieve input params and other params
-SUBJECT=$1
+SUBJECT_INPUT=$1
+# Adapting the script to handle new folder organization where each subject has multiple sessions
+SESSION_INPUT=${2:-ses-M0}  # Default to ses-M0 if not provided
+
+# Handle sct_run_batch format where SUBJECT might be "sub-001/ses-M0"
+if [[ "$SUBJECT_INPUT" == *"/"* ]]; then
+    # Extract subject and session from combined format (sct_run_batch style)
+    SUBJECT=$(echo "$SUBJECT_INPUT" | cut -d'/' -f1)
+    SESSION=$(echo "$SUBJECT_INPUT" | cut -d'/' -f2)
+    echo "Detected sct_run_batch format: $SUBJECT_INPUT -> SUBJECT=$SUBJECT, SESSION=$SESSION"
+else
+    # Use separate parameters (direct script call)
+    SUBJECT=$SUBJECT_INPUT
+    SESSION=$SESSION_INPUT
+fi
+
+# Validate parameters
+if [[ -z "$SUBJECT" ]]; then
+    echo "ERROR: SUBJECT parameter is required"
+    echo "       $0 <SUBJECT/SESSION>     (sct_run_batch format)"
+    echo "Example: $0 sub-001          (uses default ses-M0)"
+    echo "         $0 sub-001/ses-M0   (sct_run_batch format)"
+    exit 1
+fi
+
+# Verify the session directory exists (only if PATH_DATA is set)
+if [[ -n "${PATH_DATA}" && ! -d "${PATH_DATA}/${SUBJECT}/${SESSION}" ]]; then
+    echo "ERROR: Session directory ${PATH_DATA}/${SUBJECT}/${SESSION} does not exist"
+    echo "Available sessions for ${SUBJECT}:"
+    find ${PATH_DATA}/${SUBJECT} -maxdepth 1 -type d -name "ses-*" 2>/dev/null | sort || echo "  No sessions found or subject doesn't exist"
+    exit 1
+fi
+
+echo "Processing ${SUBJECT} - ${SESSION}"
 
 # get starting time:
 start=`date +%s`
@@ -104,17 +178,17 @@ fi
 
 # Copy source T2w images
 # Note: we use '/./' in order to include the sub-folder 'ses-0X'
-rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT}_*T2w.* .
+rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/${SESSION}/anat/${SUBJECT}_${SESSION}*T2w.* .
 
 # Go to subject folder for source images
-cd ${SUBJECT}/anat
+cd ${SUBJECT}/${SESSION}/anat
 
 # ------------------------------------------------------------------------------
 # T2w Sagittal
 # ------------------------------------------------------------------------------
 # Define variables
 # We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
-file_t2_sag="${SUBJECT//[\/]/_}"_acq-sagittal_T2w
+file_t2_sag="${SUBJECT//[\/]/_}"_"${SESSION}"_acq-sagittal_T2w
 # Check if file_t2_sag exists
 if [[ ! -e ${file_t2_sag}.nii.gz ]]; then
     echo "File ${file_t2_sag}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log
@@ -131,7 +205,7 @@ fi
 # ------------------------------------------------------------------------------
 # Define variables
 # We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
-file_t2_ax="${SUBJECT//[\/]/_}"_acq-axial_T2w
+file_t2_ax="${SUBJECT//[\/]/_}"_"${SESSION}"_acq-axial_T2w
 # Check if file_t2_ax exists.
 # Note: some subjects do not have T2w axial images. In this case, analysis will be stop after processing of
 # T2w sagittal image.
@@ -140,16 +214,21 @@ if [[ ! -e ${file_t2_ax}.nii.gz ]]; then
     echo "ERROR: File ${file_t2_ax}.nii.gz does not exist. Exiting."
     exit 1
 else
+    # -------------
     # Segment SC (if SC segmentation file already exists under derivatives folder, it will be copied)
+    # -------------
     segment_if_does_not_exist ${file_t2_ax} 't2'
     file_t2_ax_seg=$FILESEG
 
+    # -------------
     # Label SC
+    # TODO: consider moving the if statement inside a new function, e.g., `label_t2w_ax_if_does_not_exist`
+    # -------------
     # Check if manual disc labels file already exists. If so, generate labeled segmentation from manual disc labels.
     echo "Looking for manual disc labels: ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2_ax}_labels-manual.nii.gz"
-    if [[ -e ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2_ax}_labels-manual.nii.gz ]]; then
+    if [[ -e ${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${file_t2_ax}_labels-manual.nii.gz ]]; then
         echo "Found! Using manual disc labels."
-        rsync -avzh ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_t2_ax}_labels-manual.nii.gz ${file_t2_ax}_labels.nii.gz
+        rsync -avzh ${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${file_t2_ax}_labels-manual.nii.gz ${file_t2_ax}_labels.nii.gz
 
         file_t2_ax_labels=${file_t2_ax}_labels
     # If manual disc labels file does not exist, use disc labels from sagittal image
@@ -168,16 +247,60 @@ else
         file_t2_ax_labels=${file_t2_sag_seg}_labeled_discs_reg
     fi
 
-    # Label T2w axial spinal cord segmentation. Either using manual disc labels or using disc labels from sagittal image.
-    # Note: here we use sct_label_utils instead of sct_label_vertebrae to avoid SC straightening
-    # Context: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4072
-    sct_label_utils -i ${file_t2_ax_seg}.nii.gz -disc ${file_t2_ax_labels}.nii.gz -o ${file_t2_ax_seg}_labeled.nii.gz
+    # Label T2w axial spinal cord segmentation.
+    # Either using manual disc labels or using disc labels from sagittal image -- this is handled in the previous step.
+    # Note: we use `sct_label_vertebrae -discfile` to avoid cord straightening
+    # Details: https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4896
+    sct_label_vertebrae -i ${file_t2_ax}.nii.gz -s ${file_t2_ax_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -c t2
     # Generate QC report to assess labeled segmentation
     sct_qc -i ${file_t2_ax}.nii.gz -s ${file_t2_ax_seg}_labeled.nii.gz -p sct_label_vertebrae -qc ${PATH_QC} -qc-subject ${SUBJECT}
 
-    # Check if compression labels exists.
+    # -------------
+    # Compute spinal cord morphometrics across levels
+    # -------------
+    echo "Computing spinal cord morphometrics across vertebral levels..."
+    # Compute CSA, AP, RL, eccentricity and solidity across vertebral levels
+    sct_process_segmentation -i ${file_t2_ax_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -perlevel 1 -o ${PATH_RESULTS}/vertebral_level_metrics_cord.csv -append 1
+    # Normalized to PAM50
+    sct_process_segmentation -i ${file_t2_ax_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -normalize-PAM50 1 -perslice 1 -perlevel 1 -o ${PATH_RESULTS}/vertebral_level_metrics_cord_normalized.csv -append 1
+
+    # -------------
+    # Segment spinal canal if manual segmentation doesn't exists
+    # -------------
+    segment_canal_if_does_not_exist ${file_t2_ax} 't2'
+    file_t2_ax_canal_seg=$FILESEG
+
+    # -------------
+    # Compute spinal canal morphometrics across levels
+    # -------------
+    echo "Computing spinal canal morphometrics across vertebral levels..."
+    # Compute CSA, AP, RL across vertebral levels for canal segmentation
+    sct_process_segmentation -i ${file_t2_ax_canal_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -perlevel 1 -o ${PATH_RESULTS}/vertebral_level_metrics_canal.csv -append 1
+    # Normalized to PAM50
+    sct_process_segmentation -i ${file_t2_ax_canal_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -normalize-PAM50 1 -perslice 1 -perlevel 1 -o ${PATH_RESULTS}/vertebral_level_metrics_canal_normalized.csv -append 1
+
+    # -------------
+    # Compute aSCOR -- it needs both SC and canal segmentations
+    # -------------
+    sct_compute_ascor -i-SC ${file_t2_ax_seg}.nii.gz -i-canal ${file_t2_ax_canal_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -perlevel 1 -o ${PATH_RESULTS}/aSCOR_metrics.csv -append 1
+    # Normalized to PAM50
+    sct_compute_ascor -i-SC ${file_t2_ax_seg}.nii.gz -i-canal ${file_t2_ax_canal_seg}.nii.gz -discfile ${file_t2_ax_labels}.nii.gz -normalize-PAM50 1 -perslice 1 -perlevel 1 -o ${PATH_RESULTS}/aSCOR_metrics_normalized.csv -append 1
+
+    # -------------
+    # Segment intramedullary lesions if manual segmentation doesn't exists
+    # -------------
+    segment_lesion_if_does_not_exist ${file_t2_ax} 't2'
+    file_t2_ax_lesion_seg=$FILESEG
+    # Compute lesion metrics
+    echo "Computing lesion metrics..."
+    sct_analyze_lesion -m ${file_t2_ax_lesion_seg}_lesion_seg.nii.gz -s ${file_t2_ax_seg}.nii.gz -ofolder ${PATH_RESULTS}
+
+    # -------------
+    # Compute compression metrics
+    # -------------
+    # Check if file with compression labels exists.
     file_compression="${file_t2_ax}_label-compression-manual"
-    FILE_COMPRESSION_MANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file_compression}.nii.gz"
+    FILE_COMPRESSION_MANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${SESSION}/anat/${file_compression}.nii.gz"
     if [[ ! -e ${FILE_COMPRESSION_MANUAL} ]]; then
         echo "File ${FILE_COMPRESSION_MANUAL}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log
         echo "ERROR: File ${FILE_COMPRESSION_MANUAL}.nii.gz does not exist. Exiting."
@@ -186,8 +309,8 @@ else
         echo "Found! Using manual compression labels."
         rsync -avzh $FILE_COMPRESSION_MANUAL ${file_compression}.nii.gz
 
-        # Fetch sex from participants.tsv file
-        sex=$(grep ${SUBJECT} ${PARTICIPANTS_PATH} | awk '{print $5}')
+        # Fetch sex from participants.tsv file (adaptated for new folder organization)
+        sex=$(grep ${SUBJECT} ${PARTICIPANTS_PATH} | awk '{print $4}')
         echo "${SUBJECT}: ${sex}"
 
         # TODO: test without angle correction too
@@ -204,7 +327,6 @@ else
         sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric eccentricity -o ${PATH_RESULTS}/compression_metrics.csv
         # solidity
         sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric solidity -o ${PATH_RESULTS}/compression_metrics.csv
-
     fi
 fi
 # ------------------------------------------------------------------------------