Train a baseline model from scratch on dcm-zurich-lesions datasets using nnUNet

dataset_conversion/requirements.txt

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+loguru
+scikit-learn
+tqdm
+nibabel
+pyyaml
+collections-extended

dataset_conversion/segment_sc.sh

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+#!/bin/bash
+#
+# Run the SCIseg nnUNet model on T2w images to segment spinal cord.
+#
+# Note: conda environment with nnUNetV2 is required to run this script.
+# For details how to install nnUNetV2, see:
+# https://github.com/ivadomed/utilities/blob/main/quick_start_guides/nnU-Net_quick_start_guide.md#installation
+#
+# Usage:
+#     sct_run_batch -config config.json
+#
+# Example of config.json:
+# {
+#  "path_data"   : "<PATH_TO_DATASET>",
+#  "path_output" : "<PATH_TO_DATASET>_2024-XX-XX",
+#  "script"      : "~/code/model-seg-dcm/dataset_conversion/segment_sc",
+#  "jobs"        : 8,
+#  "script_args" : "~/code/model_seg_sci/packaging/run_inference_single_subject.py ~/models/sci-multisite-model"
+# }
+#
+# Author: Jan Valosek, Naga Karthik
+#
+
+# Uncomment for full verbose
+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
+
+# Print retrieved variables from the sct_run_batch script to the log (to allow easier debug)
+echo "Retrieved variables from from the caller sct_run_batch:"
+echo "PATH_DATA: ${PATH_DATA}"
+echo "PATH_DATA_PROCESSED: ${PATH_DATA_PROCESSED}"
+echo "PATH_RESULTS: ${PATH_RESULTS}"
+echo "PATH_LOG: ${PATH_LOG}"
+echo "PATH_QC: ${PATH_QC}"
+
+SUBJECT=$1
+PATH_NNUNET_SCRIPT=$2
+PATH_NNUNET_MODEL=$3
+
+echo "SUBJECT: ${SUBJECT}"
+echo "PATH_NNUNET_SCRIPT: ${PATH_NNUNET_SCRIPT}"
+echo "PATH_NNUNET_MODEL: ${PATH_NNUNET_MODEL}"
+
+# ------------------------------------------------------------------------------
+# CONVENIENCE FUNCTIONS
+# ------------------------------------------------------------------------------
+
+# Segment spinal cord using our nnUNet model
+segment_sc_nnUNet(){
+  local file="$1"
+  local kernel="$2"     # 2d or 3d
+
+  # output file name
+  FILESEG="${file}_seg_nnunet_${kernel}"
+
+  # Get the start time
+  start_time=$(date +%s)
+  # Run SC segmentation
+  python ${PATH_NNUNET_SCRIPT} -i ${file}.nii.gz -o ${FILESEG}.nii.gz -path-model ${PATH_NNUNET_MODEL}/nnUNetTrainer__nnUNetPlans__${kernel}_fullres -pred-type sc -use-gpu
+  # Get the end time
+  end_time=$(date +%s)
+  # Calculate the time difference
+  execution_time=$(python3 -c "print($end_time - $start_time)")
+  echo "${FILESEG},${execution_time}" >> ${PATH_RESULTS}/execution_time.csv
+
+  # Generate spinal cord QC report
+  sct_qc -i ${file}.nii.gz -s ${FILESEG}.nii.gz -p sct_deepseg_sc -qc ${PATH_QC} -qc-subject ${SUBJECT}
+  # Compute ANIMA segmentation performance metrics
+  #compute_anima_metrics ${FILESEG} ${file}_seg-manual
+}
+
+# ------------------------------------------------------------------------------
+# SCRIPT STARTS HERE
+# ------------------------------------------------------------------------------
+# 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 source T2w images
+# Note: we use '/./' in order to include the sub-folder 'ses-0X'
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+# Note: we copy only axial T2w image to save space
+rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT//[\/]/_}_*acq-ax_T2w.* .
+
+# Go to subject folder for source images
+cd ${SUBJECT}/anat
+
+# ------------------------------------------------------------------------------
+# T2w axial
+# ------------------------------------------------------------------------------
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+
+file_t2="${SUBJECT//[\/]/_}"_acq-ax_T2w
+
+# Check if file_t2 exists
+if [[ ! -e ${file_t2}.nii.gz ]]; then
+    echo "File ${file_t2}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log
+    echo "ERROR: File ${file_t2}.nii.gz does not exist. Exiting."
+    exit 1
+fi
+
+# Segment SC using the SCIseg nnUNet model
+segment_sc_nnUNet "${file_t2}" '3d'
+
+# ------------------------------------------------------------------------------
+# End
+# ------------------------------------------------------------------------------
+
+# Display results (to easily compare integrity across SCT versions)
+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 "~~~"