# Built-in commonspace template and atlas

## The DSURQE mouse atlas

By default, RABIES uses the DSURQE mouse atlas {cite}`Dorr2008-cc` - a high-resolution *ex vivo* structural MRI average of the mouse brain
accompanied with anatomical annotations provided by [the Mouse Imaging Centre (MICe)](https://www.mouseimaging.ca/) in Toronto, Canada. 
The DSURQE template, mask and label files are all automatically pulled from the [original repository](https://www.mouseimaging.ca/repo/DSURQE_40micron/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/) 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](https://doi.org/10.5281/zenodo.19069284)) 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 {cite}`Desrosiers-Gregoire2024-ou`.
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. 


```{seealso}
[How to override the default common space template](../how_to/change_template.md) for
customising the input template and associated files.
```