hi Jose,

why don't you use MNE for this? MNE is designed to work smoothly with FreeSurfer.

http://martinos.org/mne/

Cheers, Alex

On Thu, Apr 25, 2013 at 7:35 PM, José Ángel Pineda joseangel.pineda@ctb.upm.es wrote:

Dear expert,

I am doing source reconstruction with MEG.

First, I am corregistering my head surface mesh from the freesurfer (obtained with mkheadsurf) to the headshape of the subject obtained with the Polhemus tracking system.

So I already have one affine transformation (Aff_1)

The head surface was obtained over the T1 image in voxel native space (not orig.nii)

The next step is to apply an affine transformation to the T1 to bring it into the same coordinates as the headshape (and fiducials).

Then I apply Aff_1 to the T1 and check the results. I observe there is an offset displacement between the T1 and the fiducial points.

I dont know what to do to solve this. I read that as my head surface is in RAS space I should consider that, but Ive tried to correct this introducing the affine tranformation matrices that are mentioned on the web for Coordinates in Freesurfer, but Im not able to correct it.

Could you please give me any advice?

Thanks

Jose

--

José Angel Pineda Pardo

Center of Biomedical Technology (CTB)

Parque Científico y Tecnológico de la UPM

Campus de Montegancedo

28223 Pozuelo de Alarcón, Madrid, ES

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