[FieldTrip] Apply atlas to MNE grid

Wed Jun 10 21:01:17 CEST 2015

Hi Fieldtrippers,

Following the MNE-tutorial, I ended up with activation patterns on the cortically restricted grid for each subject in (if I understand it correctly) subject-specific ctf-space.
What I want to do next is apply an atlas to these grid points.

So far, what I've been doing is interpolate the subject-specific MNE grid to the subject-specific MNI-warped grid (such as the ones used for beamforming), then interpolate this to the subject-specific MRI, and finally normalize that to an MNI-space MRI, which hopefully would be atlas-compatible.
However, I am not sure whether this is a) valid, and b) the most elegant and efficient way to impart atlas information on MNE data.

a) The reason I doubt the validity of this method is that when I find high activity on the MNE grid in seemingly temporal or occipital sources, the blob on the MRI image tends to end up on the brainstem or cerebellum (an example can be seen in the attached image). Any thoughts on what could cause this? Could there for example be an issue with cerebellar grid points not being included in the MNE grid, but which are present in the beamformer/cubic grid? Do you have any thoughts on the validity of this approach and the resulting effect?

b) This pipeline feels rather contrived, with a bit too many interpolations to my liking. Is it somehow possible to shorten this pipeline? For example, is it possible to directly link the vertices of the MNE surface to an atlas?

Any thoughts or hints on this would be greatly appreciated.

Best,
Marieke
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