Fig. 1.

Pre-processing steps for the analysis of MRI scans. Image registration pipeline for T1-weighted MRI from a healthy subject to PAM50 template using the spinal cord toolbox. The original T1-weighted image (A) was segmented using deep segmentation(Perone et al., 2018) and the spinal cord mask was generated (B). Next, the template (MNI-poly T1w) was warped into subject space (C) and the T1-weighted image was warped into template space (straightened) (D). Vertebral levels were automatically labelled (E) and GM (yellow) and WM (blue) probabilistic atlases were warped back to native space (sagittal view in F) (De Leener et al., 2017). Segmented SC from C1 level down to C4 is presented in column 1. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)