Before starting this tutorialΒΆ

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:

  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

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/mt/