Transforming the GM/WM atlas to the MT space using warping fields

Now that the necessary theory has been covered, we can demonstrate how to use the PAM50 atlas to extract MTR for specific white matter tracts.

First, the white/gray matter atlas must be transformed from the unbiased PAM50 coordinate space to the space of the MT data we wish to compute metrics for. To do this, we apply a warping field (warp_template2mt.nii.gz) to the template.

sct_warp_template -d mt1.nii.gz -w warp_template2mt.nii.gz -a 1 -qc ~/qc_singleSubj

Input arguments:

• -d : Destination image the template will be warped to.

• -w : Warping field (template space to anatomical space).

• -a : Because -a 1 is specified, the white and gray matter atlas will also be warped.

• -qc : Directory for Quality Control reporting. QC reports allow us to evaluate the results slice-by-slice.

Output files/folders:

• label/template/ : This directory contains the entirety of the PAM50 template, transformed into the MT space.

• label/atlas/ : This direct contains 36 NIFTI volumes for WM/GM tracts, transformed into the MT space.

Once the command has finished, at the bottom of your terminal there will be instructions for inspecting the results using Quality Control (QC) reports. Optionally, If you have FSLeyes installed, a fsleyes command will printed as well.

Input/output images for sct_warp_template