Before starting this tutorial#
This tutorial is intended to be run following the previous Segmentation and Vertebral labeling tutorials, as registration to the PAM50 template relies on having a spinal cord segmentation mask as well as a point-label file representing vertebral level landmarks.
You can either run those tutorials first, or download the necessary files below:
Read through the following pages to familiarize yourself with key SCT concepts:
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.
single_subject/data/t2/t2_labels_vert.nii.gz: Image containing the 2 single-voxel vertebral labels
You can get these files by downloading data_template-registration.zip.
Open a terminal and navigate to the