Hi Brian,
don't know if this is still relevant for you, but if you choose the default preprocessing pipeline for volume based analyses in CONN this will already include a spatial normalization of your functional images to MNI space via the EPI template (called direct normalization, independent of the normalization of your structural images).
If you choose the second pipeline including an indirect normalization to MNI space, this will coregister your structural and functional images, normalize the structural images to MNI space and then apply the generated deformation parameters to the functional images. So your structural and functional normalization are related to some extend. This should optimally contain a phase correction using field maps, however, if those are not available, you can easily swap the first step in the analysis (realignment, unwarp, phase correction) with an individual step without phase correction (Realignment and unwarp only, found further down in the pipeline selection).
Best wishes
Julian
don't know if this is still relevant for you, but if you choose the default preprocessing pipeline for volume based analyses in CONN this will already include a spatial normalization of your functional images to MNI space via the EPI template (called direct normalization, independent of the normalization of your structural images).
If you choose the second pipeline including an indirect normalization to MNI space, this will coregister your structural and functional images, normalize the structural images to MNI space and then apply the generated deformation parameters to the functional images. So your structural and functional normalization are related to some extend. This should optimally contain a phase correction using field maps, however, if those are not available, you can easily swap the first step in the analysis (realignment, unwarp, phase correction) with an individual step without phase correction (Realignment and unwarp only, found further down in the pipeline selection).
Best wishes
Julian