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Lesion mapping

This folder contains the scripts to generate the lesion frequency map (LFM) in the PAM50 space.

Namely:

  • 01_register_to_pam50.sh: Register STIR/PSIR images to the PAM50 space and bring the GT lesion and spinal cord masks template space.
  • 02_generate_lesion_frequency_maps.py: Generate the lesion frequency map (LFM) in the PAM50 space.
  • 03_lfm_to_png.py: Save the LFM as a PNG image.

1. Register STIR/PSIR images to the PAM50 space

Register STIR/PSIR images to the PAM50 space and bring the GT lesion and spinal cord masks (located under derivatives/labels) to the PAM50 template space.

Run the script across all subjects using sct_run_batch wrapper:

sct_run_batch -config config.json

Example config.json file:

{
 "path_data"   : "<PATH_TO_DATASET>/canproco",
 "path_output" : "<PATH_TO_DATASET>/canproco_register_to_PAM50_2023-10-21",
 "script"      : "<PATH_TO_REPO>/canproco/lesion-mapping/01_register_to_pam50.sh",
 "jobs"        : 16,
 "exclude_list": "sub-mon118 sub-mon006 ..." 
}

exclude_list is used to exclude subjects from the processing, for example, due to artifacts or missing data. The subjects in the exclude_list are listed in the exclude.yml file.

2. Generate the lesion frequency map

Generate the lesion frequency map (LFM) in the PAM50 space.

ℹ️ The 02_generate_lesion_frequency_maps.py script requires the SCT conda environment to be activated:

source ${SCT_DIR}/python/etc/profile.d/conda.sh
conda activate venv_sct

Run the script:

python 02_generate_lesion_frequency_maps.py \
    -ifolder canproco_register_to_PAM50_2023-10-21/data_processed \
    -participants-tsv canproco/participants.tsv \
    -exclude-yml exclude_M0_M12_comparison.yml \
    -ofolder canproco_register_to_PAM50_2023-10-21/results \
    -session M0

3. Generate png images of the LFM

From the Lesion Frequency Map (LFM), generate:

  • axial png images for each vertebral level (average across axial slices for each vertebral level)
  • a single sagittal png image (average across sagittal slices)

ℹ️ The 03_lfm_to_png.py script requires the SCT conda environment to be activated:

source ${SCT_DIR}/python/etc/profile.d/conda.sh
conda activate venv_sct

Run the script:

python 03_lfm_to_png.py \
    -lfm-path spinalcord_LFM_MS_200_participants.nii.gz \
    -ofolder lfm \
    -thr 0.15 \
    -include-gm