[FieldTrip] mesh realignment

[Schoffelen, J.M. (Jan Mathijs)]

Dear Natalie,

I am not sure whether I understand the reason why you would want this. Could you explain why you think you’d need to ‘align’ the meshes in 3D space?

Typically, when doing a cortical mesh based source reconstruction, while at the same time using information from an (anatomical) that’s defined on a cortical mesh, the game would be to have the topologies of the meshes aligned, and not the exact position of the geometric objects. In other words, the goal (and recommended approach) is to use surface based registration techniques (and possibly re-tessellation) to have a one-to-one correspondence of the vertices in both meshes. 

If, however, you insist on doing a 3D alignment using icp (and assuming that it worked), you can apply the affine matrix to the mesh using the ft_transform_geometry function.

I would not try to do an intermediate interpolation to 3D space.

Best wishes,
Jan-Mathijs


> On 13 Apr 2020, at 10:07, Dr N.E. Adams <nea26 at cam.ac.uk> wrote:
> 
> Dear Fieldtrip Community
> 
> I would like to align two brain meshes and I can't figure out how.
> Specifically, I would like to align a MEG-coregistered segmented brain mesh that has been normalized (mesh_brain) to an atlas cortical mesh (mesh_atlas). The two meshes, in this example, are about 20mm off alignment with each other in the rostral-caudal dimensnion in the attached images and I'd like to correct for this sort of alignment issue.
> 
> Can I do this with ft_volumerealign()? If I can, I can't figure out the settings.
> 
> Attempted workaround:
> I tried using icp() to get the affine to tranform one to the other, but I do not know how to then apply this affine to meshes rather than volumes, nor if this has worked. I tried converting the mesh to a volume, but this was only partially successful and I'm unclear how to convert it back. Thinking this was a rabbit-hole I thought there must be an easier solution. Anyone know?
> 
> Thank you in advance for you help
> Natalie Adams<mesh_atlas.JPG><mesh_brain.JPG>_______________________________________________
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> https://doi.org/10.1371/journal.pcbi.1002202