run_inference_spine-generic.sh

#!/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 "~~~"