Transforming the template using warping fields

Once we have the warping field, we can use it to warp the entire template to the MT space (including vertebral levels, WM/GM atlas, and more).

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:

• 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