How to run?

This code has been tested using Python 3.7.

Download (or git clone) this repository:

git clone https://github.com/sct-pipeline/csa-atrophy.git
cd csa-atrophy

Installation: csa-atrophy requires specific python packages for computing statistics and processing images. If not already present on the computer’s python environment such packages will automatically be installed by running pip command:

pip install -e .

Download the results file from Spine Generic Multi-Subject dataset: https://github.com/spine-generic/data-multi-subject/releases/tag/r20201130 .

Edit the file config_sct_run_batch.yml according to your setup. Notable flags include:

  • path_data: If you downloaded the spine-generic data at another location, make sure to update the path;

  • include_list: If you only want to run the script in a few subjects, list them here. Example: include_list: [‘sub-unf04’, ‘sub-unf05’]

See sct_run_batch -h to look at the available options.

Run the analysis:

sct_run_batch -config config_sct_run_batch.yml

note: desired subjects using flag -include and in parallel processing using flag -jobs.

To output statistics, run in Dataset

csa_rescale_stat -i csa_atrophy_results/results -o csa_atrophy_results -config config_script.yml -fig