Before starting this tutorial

This tutorial demonstrates how to extract the MTR from specific tracts of the GM/WM atlas. Necessarily, then, we will re-use the results from the previous MTR and MT registration tutorials:

• Computing MTR using co-registration between MT0 and MT1 data

• Coregistering additional data (MT, DT) to the PAM50 template

• Reusing the GM-informed warping field to improve MTI registration

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/mt/mt1.nii.gz: A magnetization transfer image with the off-resonance RF pulse applied.

   • single_subject/data/mt/mtr.nii.gz: An image containing the voxel-wise magnetization transfer ratio.

   • single_subject/data/mt/warp_template2mt.nii.gz : The 4D warping field that defines the transform from the template image to the MT image.

   You can get these files by downloading data_atlas-based-analysis.zip.

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/mt/