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

---------------------------------------------------------------- David Hawellek Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg, Germany +4940 7410 55132 d.hawellek@uke.uni-hamburg.de ----------------------------------------------------------------