Before starting this tutorialΒΆ
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:
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.
Open a terminal and navigate to the
single_subject/data/t2s/
directory:
cd {PATH_TO_DOWNLOADED_DATA}/single_subject/data/t2s/