Fig. 3
From: Guidelines for the conduct of clinical trials in spinal cord injury: Neuroimaging biomarkers
Overview of a template-based analysis pipeline using SCT: On the far right the PAM50 spinal cord template (orange box) and the MNI brain template (red box) are shown. First, anatomical data (e.g., T1-weighted or T2-weighted scans at 1 mm isotropic resolution or similar) is registered to the template (blue arrows). Additional quantitative MRI data acquired during the same scan session (e.g., DTI, magnetisation transfer, and fMRI) are registered to the anatomical data, and then template objects are warped to the multi-parametric data (green arrows). To improve accuracy of template registration, it is possible to add a step where the gray matter is segmented [66] and then warped to the gray matter template in order to update the warping fields (purple arrows). Subsequently, those MRI metrics can be quantified within specific WM tracts (red arrows). Cross-sectional area (CSA) of the spinal cord and gray matter can also be computed across vertebral levels. Adapted with permission [33]
