Merge pull request #50 from sct-pipeline/sb/process_pathology

Add processing of datasets with pathology

README.md

@@ -127,3 +127,8 @@ python gen_charts.py --contrasts T1w T2w T2star rec-average_dwi \
        --predictions_folder ../duke/projects/ivadomed/contrast-agnostic-seg/csa_measures_pred/group8-9_combined-2022-12-21/ \
        --baseline_folder ../duke/projects/ivadomed/contrast-agnostic-seg/archive_derivatives_softsegs-seg/contrast-agnostic-centerofmass-preprocess-clean-all-2022-10-22\results_MTS_renamed
 ```
+## Run qc report on prediction masks
+
+~~~
+sct_run_batch -path-data <PATH_DATA> -path-out <PATH-OUT> -script-args <PATH_PRED_MASK> -jobs 20 -script run_qc_prediction.sh
+~~~

run_qc_prediction.sh

@@ -0,0 +1,102 @@
+#!/bin/bash
+#
+# Run QC report on prediction masks
+# Usage:
+#   ./run_qc_prediction.sh <SUBJECT>
+#
+#
+# Authors: Sandrine Bédard
+#
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+# PATH_DATA_PROCESSED="~/data_processed"
+# PATH_RESULTS="~/results"
+# PATH_LOG="~/log"
+# PATH_QC="~/qc"
+
+set -x
+# Immediately exit if error
+set -e -o pipefail
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+PATH_PRED_SEG=$2
+
+# get starting time:
+start=`date +%s`
+
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd ${PATH_DATA_PROCESSED}
+# Copy list of participants in processed data folder
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+# Copy list of participants in resutls folder
+if [[ ! -f $PATH_RESULTS/"participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv $PATH_RESULTS/"participants.tsv"
+fi
+
+# Copy source images
+# Copy session if specified
+if [[ $SUBJECT == *"ses"* ]];then
+    rsync -Ravzh $PATH_DATA/./$SUBJECT .
+else
+    rsync -avzh $PATH_DATA/$SUBJECT .
+fi
+
+
+# FUNCTIONS
+# ==============================================================================
+
+find_contrast(){
+  local file="$1"
+  local dwi="dwi"
+  if echo "$file" | grep -q "$dwi"; then
+    echo  "./${dwi}/"
+  else
+    echo "./anat/"
+  fi
+}
+
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Go to anat folder where all structural data are located
+cd ${SUBJECT}
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+file_sub="${SUBJECT//[\/]/_}"
+
+for file_pred in ${PATH_PRED_SEG}/*; do
+    if [[ $file_pred == *$file_sub* ]];then
+        echo " File found, running QC report $file_pred"
+        # Find if anat or dwi
+        file_seg_basename=${file_pred##*/}
+        echo $file_seg_basename
+        type=$(find_contrast $file_path)
+        # rsync prediction mask
+        rsync -avzh $file_pred ${type}/$file_seg_basename
+        file_image=${file_seg_basename//"_class-0_pred"}
+        echo $file_image
+        # Create QC for pred mask
+        sct_qc -i ${type}/${file_image} -s ${type}/${file_seg_basename} -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
+
+
+    fi
+done
+#TODO find anat or dwi
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"

scripts/process_data_basel_mp2rage.sh

@@ -0,0 +1,141 @@
+#!/bin/bash
+#
+# Process data from sci-colorado
+#     Crop all images.
+# Authors: Sandrine Bédard
+
+# The following global variables are retrieved from the caller sct_run_batch
+# but could be overwritten by uncommenting the lines below:
+# PATH_DATA_PROCESSED="~/data_processed"
+# PATH_RESULTS="~/results"
+# PATH_LOG="~/log"
+# PATH_QC="~/qc"
+
+# Uncomment for full verbose
+set -x
+
+# Immediately exit if error
+#set -e -o pipefail --> will not enter in the loop if so...
+
+# Exit if user presses CTRL+C (Linux) or CMD+C (OSX)
+trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT
+
+# Retrieve input params
+SUBJECT=$1
+
+# get starting time:
+start=`date +%s`
+
+# SCRIPT STARTS HERE
+# ==============================================================================
+# Display useful info for the log, such as SCT version, RAM and CPU cores available
+sct_check_dependencies -short
+
+# Go to folder where data will be copied and processed
+cd $PATH_DATA_PROCESSED
+# Copy list of participants in processed data folder
+if [[ ! -f "participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv .
+fi
+if [[ ! -f "participants.json" ]]; then
+  rsync -avzh $PATH_DATA/participants.json .
+fi
+if [[ ! -f "dataset_description.json" ]]; then
+  rsync -avzh $PATH_DATA/dataset_description.json .
+fi
+if [[ ! -f "README.md" ]]; then
+  rsync -avzh $PATH_DATA/README.md .
+fi
+# Copy list of participants in results folder
+if [[ ! -f $PATH_RESULTS/"participants.tsv" ]]; then
+  rsync -avzh $PATH_DATA/participants.tsv $PATH_RESULTS/"participants.tsv"
+fi
+# Copy source images
+rsync -avzh $PATH_DATA/$SUBJECT .
+
+
+# FUNCTIONS
+# ==============================================================================
+segment_if_does_not_exist(){
+  local file="$1"
+  local contrast="$2"
+  local contrast_for_seg="$3"
+  # Find contrast
+  if [[ $contrast == "./dwi/" ]]; then
+    folder_contrast="dwi"
+  else
+    folder_contrast="anat"
+  fi
+
+  # Update global variable with segmentation file name
+  FILESEG="${file}_label-SC_seg"
+  FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/${folder_contrast}/${FILESEG}.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}
+  else
+    echo "Manual segmentation not found."
+    # Segment spinal cord
+    sct_deepseg_sc -i ${file}.nii.gz -c $contrast_for_seg -qc ${PATH_QC} -qc-subject ${SUBJECT} -o ${FILESEG}.nii.gz
+
+  fi
+}
+
+# Go to anat folder where all structural data are located
+cd ${SUBJECT}/anat/
+
+
+# MP2RAGE
+# ------------------------------------------------------------------------------
+file_mp2rage="${SUBJECT}_UNIT1"
+segment_if_does_not_exist ${file_mp2rage} 'anat' 't1'
+
+file_path=$file_mp2rage
+fileseg="${file_mp2rage}_label-SC_seg"
+# Crop image 
+sct_crop_image -i ${file_path}.nii.gz -dilate 7 -m ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${fileseg}.nii.gz -o ${file_path}_crop.nii.gz
+# Crop segmentation
+sct_crop_image -i ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${fileseg}.nii.gz -dilate 7 -m ${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${fileseg}.nii.gz -o ${fileseg}_crop.nii.gz
+
+# Go back to root output folder
+cd $PATH_OUTPUT
+# Create and populate clean data processed folder for training
+PATH_DATA_PROCESSED_CLEAN="${PATH_DATA_PROCESSED}_clean"
+# Copy over required BIDs files
+rsync -avzh $PATH_DATA_PROCESSED/dataset_description.json $PATH_DATA_PROCESSED_CLEAN/
+rsync -avzh $PATH_DATA_PROCESSED/participants.* $PATH_DATA_PROCESSED_CLEAN/
+rsync -avzh $PATH_DATA_PROCESSED/README.md $PATH_DATA_PROCESSED_CLEAN/
+rsync -avzh $PATH_DATA_PROCESSED/dataset_description.json $PATH_DATA_PROCESSED_CLEAN/
+mkdir -p $PATH_DATA_PROCESSED_CLEAN $PATH_DATA_PROCESSED_CLEAN/${SUBJECT}/anat $PATH_DATA_PROCESSED_CLEAN/derivatives/labels/${SUBJECT}/anat
+# Put cropped image and json in cleaned dataset
+rsync -avzh $PATH_DATA_PROCESSED/${SUBJECT}/anat/${file_path}_crop.nii.gz $PATH_DATA_PROCESSED_CLEAN/${SUBJECT}/anat/${file_path}.nii.gz
+#rsync -avzh $PATH_DATA_PROCESSED/${SUBJECT}/anat/${file_path}.json $PATH_DATA_PROCESSED_CLEAN/${SUBJECT}/anat/${file_path}.json
+# Move segmentation
+rsync -avzh $PATH_DATA_PROCESSED/${SUBJECT}/anat/${fileseg}_crop.nii.gz $PATH_DATA_PROCESSED_CLEAN/derivatives/labels/${SUBJECT}/anat/${fileseg}.nii.gz
+# Move json files of derivatives
+rsync -avzh "${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${fileseg}.json" $PATH_DATA_PROCESSED_CLEAN/derivatives/labels/${SUBJECT}/anat/${fileseg}.json
+
+# Verify presence of output files and write log file if error
+# ------------------------------------------------------------------------------
+FILES_TO_CHECK=(
+  "${SUBJECT}_UNIT1.nii.gz"
+)
+pwd
+for file in ${FILES_TO_CHECK[@]}; do
+  if [[ ! -e $file ]]; then
+    echo "${SUBJECT}/anat/${file} does not exist" >> $PATH_LOG/_error_check_output_files.log
+  fi
+done
+
+# Display useful info for the log
+end=`date +%s`
+runtime=$((end-start))
+echo
+echo "~~~"
+echo "SCT version: `sct_version`"
+echo "Ran on:      `uname -nsr`"
+echo "Duration:    $(($runtime / 3600))hrs $((($runtime / 60) % 60))min $(($runtime % 60))sec"
+echo "~~~"