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dprice80 / mni2fs

MNI2FS: Surface Rendering of MNI Space Volumes for MATLAB
GNU General Public License v3.0
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Transformation matrices in 'surf'transmats.mat'? #11

Closed cmicek1 closed 6 years ago

cmicek1 commented 6 years ago

Hi Darren, could you elaborate on what each of the transformation matrices are in 'surf/transmats.mat'? The data I'm working with is a list of values for vertices of a different mesh that have coordinates in MNI-space (I believe with the origin in the top-right), and it would be great if I could convert these points into points on the FreeSurfer surface without having to first convert them into a NIFTI volume.

cmicek1 commented 6 years ago

Also, I'm assuming this is the case but maybe you can clarify: The surface you have included is of the MNI brain, correct?

dprice80 commented 6 years ago

The surface is the colin27 brain extracted using freesurfer. It's the same canonical brain used in SPM and Fieldtrip, although I downloaded the full resolution version, and reduced the number of vertices using freesurfer decimation.

There should be a publication soon to explain all of this.

Thanks Darren

On 22 June 2018 at 17:46, Christopher Micek notifications@github.com wrote:

Also, I'm assuming this is the case but maybe you can clarify: The surface you have included is of the MNI brain, correct?

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dprice80 commented 6 years ago

Sorry I've just realised this draft may not have been sent....

To do this you would need to coregister the surfaces in freesurfer. There is no straightforward way to map from one surface to another if they do not have the same vertex coordinates. If the vertices are very close you could do nearest neighbour interpolation quite easily but depends on your needs. The surface used in mni2fs is the colin27 brain.

Darren

On Fri, 8 Jun 2018, 23:18 Christopher Micek, notifications@github.com wrote:

Hi Darren, could you elaborate on what each of the transformation matrices are in 'surf/transmats.mat'? The data I'm working with is a list of values for vertices of a different mesh that have coordinates in MNI-space (I believe with the origin in the top-right), and it would be great if I could convert these points into points on the FreeSurfer surface without having to first convert them into a NIFTI volume.

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cmicek1 commented 6 years ago

Sweet, thanks! I did start out doing interpolation to start with, but it was pretty slow so what I wound up doing was substituting the Freesurfer surface in place of our initial surface in our pipeline, and that has been working pretty smoothly so far.