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:
You can either run those tutorials first, or download the necessary files below:
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.
Open a terminal and navigate to the