Before starting this tutorial#

This compression analysis tutorial is separate from the previous segmentation, labeling, and shape analysis tutorials, meaning it can be run standalone.

  1. Make sure that you have the following files in your working directory:

    • single_subject/data/t2_compression/t2_compression.nii.gz: A 3D binary mask for the spinal cord of a T2w anatomical image with spinal cord compression.

    You can get these files by downloading

  2. Open a terminal and navigate to the single_subject/data/t2_compression/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2_compression/