Before starting this tutorial#

This tutorial is intended to be run following the previous Segmenting the gray and white matter for T2* data tutorial, as GM/WM metric computation relies on having segmentation masks of the grey and white matter.

You can either run that tutorials first, or download the necessary files below:

  1. Make sure that you have the following files in your working directory:

    • 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.

    • single_subject/data/t2s/t2s_gmseg.nii.gz: A binary mask for the gray matter segmentation of the spinal cord.

    You can get these files by downloading data_gm-wm-metric-computation.zip.

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

cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2s/