Atlas-based analysis#

While it can be helpful to extract metrics using the white and gray matter segmentations alone (as was shown in the Computing metrics using GM and WM segmentations tutorial), there is additional value in extracting metrics from more specific regions of the white and gray matter (e.g. individual tracts). This can be done using an atlas.

In SCT, a digitalized version of the Gray’s Anatomy spinal cord white matter atlas [Standring, Gray’s Anatomy 2008] was merged with the PAM50 Template. For more information on the procedure, see [Lévy et al., Neuroimage 2015].

https://raw.githubusercontent.com/spinalcordtoolbox/doc-figures/master/pam50/white_matter_atlas_detailed.png

The atlas is composed of 30 WM tracts, 6 GM regions and the surrounding CSF. The reason for including the CSF is to be able to account for the partial volume effect during metric estimation.