Before starting this tutorial¶
Make sure that you have the following files in your working directory:
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/label/template/PAM50_levels.nii.gz: A PAM50 template object containing vertebral levels, that has been transformed to the space of the T2 anatomical image.
You can get these files by downloading data_shape-metric-computation.zip.
Open a terminal and navigate to the