Run SCIsegV2 inference on spine-generic

baselines/run_inference_spine-generic.sh

@@ -0,0 +1,95 @@
+#!/bin/bash
+#
+# Segment SC and lesions using our nnUNet SCIsegV2 model (part of SCT v6.4) on spine-generic multi-subject T2w iso images 
+# and generate QC report
+#
+# Usage:
+#     sct_run_batch -config config.json
+#
+# Example of config.json:
+# {
+#  "path_data"   : "data-multi-subject",
+#  "path_output" : "data-multi-subject_2024-08-25",
+#  "script"      : "<PATH_TO_REPO>/model_seg_sci/baselines/run_inference_spine-generic.sh",
+#  "jobs"        : 8
+# }
+#
+#
+# Author: Jan Valosek
+#
+
+# 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
+
+echo "SUBJECT: ${SUBJECT}"
+
+# ------------------------------------------------------------------------------
+# 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/'
+# copy only T2w to save space
+rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT//[\/]/_}_*T2w.* .
+
+# Go to subject folder for source images
+cd ${SUBJECT}/anat
+
+# ------------------------------------------------------------------------------
+# T2w
+# ------------------------------------------------------------------------------
+
+# We do a substitution '/' --> '_' in case there is a subfolder 'ses-0X/'
+file_t2="${SUBJECT//[\/]/_}"_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
+else
+    # Segment SC and lesion using SCIsegV2 (part of SCT v6.4)
+    # Note: a single axial QC report contains both SC and lesion segmentations
+    # Note: we use CUDA_VISIBLE_DEVICES=0 SCT_USE_GPU=1 to run the inference on GPU 0; details:
+    # https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/4421#issuecomment-2263344151
+    CUDA_VISIBLE_DEVICES=0 SCT_USE_GPU=1 sct_deepseg -i ${file_t2}.nii.gz -task seg_sc_lesion_t2w_sci -qc ${PATH_QC} -qc-subject ${SUBJECT}
+fi
+
+# ------------------------------------------------------------------------------
+# End
+# ------------------------------------------------------------------------------
+
+# Display results (to easily compare integrity across SCT versions)
+end=`date +%s`
+runtime=$((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 "~~~"