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?

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:

-1 0 0 91

0 1 0 -127

0 0 1 -73

0 0 0 1

For the surface I can get the ori.mgz transformation:

-1 0 0 128

0 0 1 -146

0 -1 0 148

0 0 0 1

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

Thank you

Dorothy

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer