Before starting this tutorial

This tutorial is intended to be run following the previous Segmentation and Vertebral labeling tutorials, as shape analysis relies on having a spinal cord segmentation mask as well as intervertebral disc labels.

You can either run those tutorials first, or download the necessary files below:

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

   • single_subject/data/t2/t2.nii.gz: An anatomical spinal cord scan in the T2 contrast.

   • single_subject/data/t2/t2_seg.nii.gz: A 3D binary mask for the spinal cord of a T2 anatomical image.

   • single_subject/data/t2/t2_totalspineseg_discs.nii.gz: An image containing intervertebral disc labels.

   You can get these files by downloading data_shape-metric-computation.zip.

2. Open a terminal and navigate to the single_subject/data/t2/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2/