Built-in commonspace template and atlas

The DSURQE mouse atlas

By default, RABIES uses the DSURQE mouse atlas [DLS+08] - a high-resolution ex vivo structural MRI average of the mouse brain accompanied with anatomical annotations provided by the Mouse Imaging Centre (MICe) in Toronto, Canada. The DSURQE template, mask and label files are all automatically pulled from the original repository upon installing RABIES.

The EPICOMMON mouse template

When using the --bold_only parameter to execute RABIES without structural scans, the common space template file is changed for an alternative EPI reference template. This so-called EPICOMMON template (available on zenodo) was generated by executing the initial stages of the --bold_only RABIES preprocessing - 3D EPI generation, EPI inhomogeneity correction and unbiased template generation from the EPI - using 5 independent fMRI datasets from different sites [DGregoireDGC24]. The EPI template then inherited all mask and label files from the DSURQE atlas through non-linear registration.

Providing an EPI template as target greatly improves the robustness of EPI registration, since image contrast and shape are much more similar.