You can create individual labels with mri_annotation2label from the fsaverage annotation. The label is a text file with coordinate in it. The coordinates will be MNI305 space. You can read these into matlab with read_label.m. These will need to be converted to MNI152. See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems, example 8. You can then compute the centroid or average or whatever.

Hi All, 

I am trying to visualise nodes of a brain network reconstructed using FreeSurfer Desikan-Killiany Atlas parcellation scheme (aparc+aseg.mgz) on Brain Net Viewer and Network Based Statistics software. 

In order to do so, I need to upload a .txt file listing Freesurfer labels coordinates in MNI space. Is there any way I can get a list of MNI coordinates for my set of labels?

Many thanks,

Theo

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