Hello there,
I'd like to extract standard space coordinates (in the end I would
like to use MNI coods) for each vertex of a structure of an anatomical
parcellation. This so far seems pretty straight forward from what I
read, but I somehow got lost between coordinate systems while doing
the following:
- Having an aparc.annot file I created a .label file for each
structure using mri_annotation2label (with the pial surface).
- After reading the comments by Darren Weber, I used mris_info to get
the transformation from the surfaceRAS to talairached surface RAS
coordinates and applied it to the data in the label files in Matlab
(Using read_label.m and Darren's freesurfer_label2tal.m instructions).
- In order to get the information to MNI space then, I simply used
tal2mni.m.
What I see is not totally absurd, but I noticed a slight backward
shift. Is it that I'm lacking a further transformation for the surface
coordinates? Or do you perhaps even know a more elegant way of doing
this?
Thanks for the support!
David
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David Hawellek
Dept. of Neurophysiology and Pathophysiology
University Medical Center Hamburg-Eppendorf
Martinistr. 52
20246 Hamburg, Germany
+4940 7410 55132
d.hawel...@uke.uni-hamburg.de
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