I don't know anythinga about fieldtrip, and the discrepancy could be in they way it interprets coordsinates. See this

https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems

Does it look ok if you look at it in freeview?

On 12/28/17 7:29 PM, Dorothy Sincasto wrote:

Hi

I've been struggling to convert a freesurfer surface into an MNI space coordinate. I tried to follow some tutorials and to play around with transformation matrices but nothing works.

I have an MNI surface from freesurfer (the cvs_avg35_inMNI152) and I need to align it to the 3d MNI 152. When loading them with fieldtrip it almost matches as can be seen in the picture https://ibb.co/evkcRb

I would like to apply a transformation to align the surface to the volume.

For the 3d MNI I have the transformation matrix: -10091 010-127 001-73 0001

For the surface I can get the ori.mgz transformation: -100128 001-146 0-10148 0001

Could someone point me out how to convert the FS surface into spm coordinates?

Thank you Dorothy

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