Before starting this tutorial¶
Make sure that you are working with a copy of SCT 6.1 or higher, and have an up-to-date copy of the PAM50 template:
sct_download_data -d PAM50
For older versions of SCT, you can download the latest release of the PAM50 template manually, then copy the files into the
$SCT_DIR/data/PAM50folder. (We recommend making a backup of the PAM50 folder if you are performing ongoing work with a stable release of SCT, that way you can go back to the older copy when resuming your work.)
Make sure that you have the following files in your working directory:
single_subject/data/t2_lumbar/t2_lumbar.nii.gz: T2w anatomical scan of the lumbar spinal cord.
You can get this file by downloading data_lumbar-registration.zip.
Open a terminal and navigate to the