Before starting this tutorial

This tutorial demonstrates how to use the GM/WM information obtained from the T2s contrast to improve registration for other types of contrasts.

This means that we will be re-using the files generated in previous registration tutorials, as well as the segmentation from the previous GM/WM segmentation tutorial:

• T2 files: Registering labeled anatomical images to the PAM50 template

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

• T2s files: Segmenting the gray and white matter for T2* data

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:

   • T2 and T2* files (used in the initial registration to template for T2* data)

     • single_subject/data/t2/warp_anat2template.nii.gz : The 4D warping field that defines the transform from a T2 anatomical image to the template image.

     • single_subject/data/t2/warp_template2anat.nii.gz : The 4D warping field that defines the inverse transform from the template image to a T2 anatomical image.

     • single_subject/data/t2s/t2s.nii.gz : A T2* anatomical image of the spinal region.

     • single_subject/data/t2s/t2s_wmseg.nii.gz: A binary mask for the white matter segmentation of the spinal cord.

   • MT files (used when improving MT registration with T2* warping fields)

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

     • single_subject/data/mt/mt1_seg.nii.gz : 3D segmentation of the spinal cord, corresponding to the MT1 image.

     • single_subject/data/mt/mask_mt1.nii.gz : 3D binary mask surrounding the segmented spinal cord, corresponding to the MT1 image.

   You can get these files by downloading data_improving-registration-with-gm-seg.zip.

2. Open a terminal and navigate to the single_subject/data/t2s/ directory:

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2s/