Hello,

 

I have an fsaverage5 parcellation/annotation based on Schaefer 200 (attached). The parcel boundaries are supposed to be adjusted iteratively resulting in 200 contiguous parcels with new boundaries. In this person, it is clear from plotting in freeview that 1 vertex from a visual parcel migrated to be surrounded by the SOM (blue) and VAN (violet) network on the lateral side (same hemisphere). This doesn’t happen in all subjects, so I’d like to write a function to find this and similar parcels that are not contiguous in a more automated fashion.

 

So far, I’ve used the matlab read_annotation.m function to count vertices per parcel but that’s not quite right because it treats all vertices with the same label as the same thing. Not sure if there is a way to identify neighboring vertices so I can see if any have the same label (contiguous) or not.

 

I investigated mri_surfcluster but I’m not sure how to make it treat the annotation as the input. Perhaps there is a way to project the values (1-200) associated with each label to their vertices. And then mri_surfcluster requires contiguity so it may identify if there is a mismatch between the expected # of parcels and observed # of clusters.

 

I am using freesurfer 7.3.2, Matlab 2020a, M1 iMac.

 

Any thoughts on how to identify non-contiguous vertices within a parcellation?

 

Thank you,

Colleen

 

McGill University