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Register PSIR/STIR to PAM50 and generate lesion frequency maps (#67)
* add `01_register_to_pam50.sh` * add `02_generate_lesion_frequency_maps.py` * add `03_lfm_to_png.py`
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| #!/bin/bash | ||
| # | ||
| # Register PSIR/STIR contrasts to PAM50 space using the spinal cord segmentation and disc labels | ||
| # Then, use the transformation to bring the GT lesion to PAM50 space | ||
| # | ||
| # NOTE: the commands below assume that GT SC and lesion segmentation and manual disc labels are located under | ||
| # derivatives/labels | ||
| # | ||
| # Usage: | ||
| # sct_run_batch -config config.json | ||
| # | ||
| # | ||
| # Example of config.json: | ||
| # { | ||
| # "path_data" : "<PATH_TO_DATASET>/canproco", | ||
| # "path_output" : "<PATH_TO_DATASET>/canproco_register_to_PAM50_2023-10-21", | ||
| # "script" : "<PATH_TO_REPO>/canproco/segment_sc_contrast-agnostic/01_register_to_pam50.sh", | ||
| # "jobs" : 16, | ||
| # "exclude_list" : "sub-mon118 sub-mon006 ..." | ||
| # } | ||
| # | ||
| # 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" | ||
| # | ||
| # Author: Jan Valosek | ||
| # | ||
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| # Uncomment for full verbose | ||
| set -x | ||
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| # Immediately exit if error | ||
| set -e -o pipefail | ||
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| # Exit if user presses CTRL+C (Linux) or CMD+C (OSX) | ||
| trap "echo Caught Keyboard Interrupt within script. Exiting now.; exit" INT | ||
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| # 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}" | ||
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| SUBJECT=$1 | ||
| PATH_SCRIPT=$2 | ||
| PATH_MODEL=$3 | ||
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| echo "SUBJECT: ${SUBJECT}" | ||
| echo "PATH_SCRIPT: ${PATH_SCRIPT}" | ||
| echo "PATH_MODEL: ${PATH_MODEL}" | ||
|
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| # ------------------------------------------------------------------------------ | ||
| # CONVENIENCE FUNCTIONS | ||
| # ------------------------------------------------------------------------------ | ||
|
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| # Copy GT lesion segmentation | ||
| copy_gt(){ | ||
| local file="$1" | ||
| local type="$2" # seg or lesion | ||
| # Construct file name to GT lesion segmentation located under derivatives/labels | ||
| FILESEGMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${file}_${type}-manual.nii.gz" | ||
| echo "" | ||
| echo "Looking for manual segmentation: $FILESEGMANUAL" | ||
| if [[ -e $FILESEGMANUAL ]]; then | ||
| echo "Found! Copying ..." | ||
| rsync -avzh $FILESEGMANUAL ${file}_${type}-manual.nii.gz | ||
| else | ||
| echo "File ${FILESEGMANUAL}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log | ||
| echo "ERROR: Manual GT segmentation ${FILESEGMANUAL}.nii.gz does not exist. Exiting." | ||
| exit 1 | ||
| fi | ||
| } | ||
|
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| # Copy manually created disc labels from derivatives/labels | ||
| copy_disc_labels(){ | ||
| local file="$1" | ||
| # Update global variable with disc labels file name | ||
| FILELABEL="${file}_labels-disc" | ||
| FILELABELMANUAL="${PATH_DATA}/derivatives/labels/${SUBJECT}/anat/${FILELABEL}.nii.gz" | ||
| echo "Looking for manual disc labels: $FILELABELMANUAL" | ||
| if [[ -e $FILELABELMANUAL ]]; then | ||
| echo "Found! Copying manual disc labels." | ||
| rsync -avzh $FILELABELMANUAL ${FILELABEL}.nii.gz | ||
| else | ||
| echo "File ${FILESEGMANUAL}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log | ||
| echo "ERROR: Manual disc labels ${FILESEGMANUAL}.nii.gz does not exist. Exiting." | ||
| exit 1 | ||
| fi | ||
| } | ||
|
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| # ------------------------------------------------------------------------------ | ||
| # SCRIPT STARTS HERE | ||
| # ------------------------------------------------------------------------------ | ||
| # get starting time: | ||
| start=`date +%s` | ||
|
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| # Display useful info for the log, such as SCT version, RAM and CPU cores available | ||
| sct_check_dependencies -short | ||
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| # Go to folder where data will be copied and processed | ||
| cd $PATH_DATA_PROCESSED | ||
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| # Copy source PSIR/STIR images | ||
| # Note: we use '/./' in order to include the sub-folder 'ses-M0' | ||
| # We do a substitution '/' --> '_' in case there is a subfolder 'ses-M0/' | ||
| rsync -Ravzh ${PATH_DATA}/./${SUBJECT}/anat/${SUBJECT//[\/]/_}_*IR.* . | ||
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| # Go to subject folder for source images | ||
| cd ${SUBJECT}/anat | ||
|
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| # ------------------------------------------------------------------------------ | ||
| # PSIR/STIR | ||
| # ------------------------------------------------------------------------------ | ||
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| # We do a substitution '/' --> '_' in case there is a subfolder 'ses-M0/' | ||
| # Calgary has STIR | ||
| if [[ ${SUBJECT} =~ "cal" ]]; then | ||
| file="${SUBJECT//[\/]/_}"_STIR | ||
| # Other sites have PSIR | ||
| else | ||
| file="${SUBJECT//[\/]/_}"_PSIR | ||
| fi | ||
|
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| # Check if file exists | ||
| if [[ ! -e ${file}.nii.gz ]]; then | ||
| echo "File ${file}.nii.gz does not exist" >> ${PATH_LOG}/missing_files.log | ||
| echo "ERROR: File ${file}.nii.gz does not exist. Exiting." | ||
| exit 1 | ||
| else | ||
|
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| # Create a variable with fname corresponding to the files under derivatives/labels (because we modify the variable | ||
| # for PSIR images) | ||
| file_gt=${file} | ||
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| if [[ ${file} =~ "PSIR" ]]; then | ||
| # For PSIR, swap contrast from light cord and dark CSF to dark cord and light CSF to use -c t2 during template registration | ||
| # Context: https://github.com/ivadomed/canproco/issues/46#issuecomment-1752142304 | ||
| # TODO: this line will be deleted once the SCT script will include the flag for contrast swapping | ||
| sct_maths -i ${file}.nii.gz -mul -1 -o ${file}_mul.nii.gz | ||
| file=${file}_mul | ||
| fi | ||
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| # NOTE: the commands below assume that GT SC, GT lesion segmentation and manual disc labels are located under | ||
| # derivatives/labels | ||
| # Copy GT SC seg | ||
| copy_gt "${file_gt}" "seg" | ||
| file_seg="${file_gt}_seg-manual" | ||
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| # Copy GT lesion seg | ||
| copy_gt "${file_gt}" "lesion" | ||
| file_lesion="${file_gt}_lesion-manual" | ||
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| # Copy manually created disc labels from derivatives/labels | ||
| copy_disc_labels "${file_gt}" | ||
| file_disc="${file_gt}_labels-disc" | ||
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| # Binarize GT lesion segmentation | ||
| sct_maths -i ${file_lesion}.nii.gz -bin 0 -o ${file_lesion}_bin.nii.gz | ||
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| # Register to template | ||
| # The flag '-param' is inspired by: Eden, D. et al. Brain, 2019. https://doi.org/10.1093/brain/awy352 | ||
| # https://github.com/neuropoly/lesion-mapping/blob/497584281526bbcee2f56bfa9ec076982c7f1503/spinalcord/1_register_data.py#L22 | ||
| # Note: we use '-ldisc' to use all disc labels | ||
| sct_register_to_template -i ${file}.nii.gz -s ${file_seg}.nii.gz -ldisc ${file_disc}.nii.gz -c t2 -param step=1,type=seg,algo=centermass,metric=MeanSquares,slicewise=1:step=2,type=seg,algo=bsplinesyn,metric=MeanSquares,slicewise=1,iter=3 -qc ${PATH_QC} -qc-subject ${SUBJECT} | ||
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| # Generate additional QC to check the registration | ||
| # Native image in PAM50 space | ||
| # https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4166#issuecomment-1773808040 | ||
| sct_qc -i ${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz -d anat2template.nii.gz -p sct_image_stitch -qc ${PATH_QC} -qc-subject ${SUBJECT} | ||
| # Native image in PAM50 space overlaid with PAM50_levels | ||
| # https://github.com/spinalcordtoolbox/spinalcordtoolbox/issues/4166#issuecomment-1773810021 | ||
| sct_qc -i anat2template.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_levels.nii.gz -p sct_label_vertebrae -qc ${PATH_QC} -qc-subject ${SUBJECT} | ||
|
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| # Bring GT lesion segmentation to template space | ||
| sct_apply_transfo -i ${file_lesion}_bin.nii.gz -d ${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz -w warp_anat2template.nii.gz -x linear -o ${file_lesion}_bin_reg.nii.gz | ||
| # Generate QC (native image in PAM50 space overlaid with GT lesion segmentation in PAM50 space) | ||
| sct_qc -i anat2template.nii.gz -d ${file_lesion}_bin_reg.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz -p sct_deepseg_lesion -plane sagittal -qc ${PATH_QC} -qc-subject ${SUBJECT} | ||
|
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| # Bring GT SC segmentation to template space | ||
| sct_apply_transfo -i ${file_seg}.nii.gz -d ${SCT_DIR}/data/PAM50/template/PAM50_t2.nii.gz -w warp_anat2template.nii.gz -x linear -o ${file_seg}_reg.nii.gz | ||
| # Generate QC (native image in PAM50 space overlaid with GT SC segmentation in PAM50 space) | ||
| sct_qc -i anat2template.nii.gz -d ${file_seg}_reg.nii.gz -s ${SCT_DIR}/data/PAM50/template/PAM50_cord.nii.gz -p sct_deepseg_lesion -plane sagittal | ||
| fi | ||
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| # ------------------------------------------------------------------------------ | ||
| # End | ||
| # ------------------------------------------------------------------------------ | ||
|
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| # Display results (to easily compare integrity across SCT versions) | ||
| end=`date +%s` | ||
| runtime=$((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 "~~~" |
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