Hi Keith,

The problem is actually the outer_skin crossing the outer_skull surface (from the images you show). For future data you will want to do a better job aligning the slices for the MRI to make sure you are well below the cerebellum in your coverage.

For this participant's data. you can load up the T1 in freeview, and edit the voxels at the base of the head to draw in a skin layer well below the cerebellum that connects to the person's skin at the neck.

hth
d

On Tue, Jan 26, 2016 at 2:14 PM, Keith Doelling <kd889@nyu.edu> wrote:
Hi All,

I'm trying to source localize MEG data in MNE-Python but have run across an issue with a subject's MRI in the freesurfer watershed algorithm. Namely, the outer skull surface ever so slightly overlaps with the inner skull  (I've plotted this in freeview for your viewing pleasure). This is a problem as MNE stops with an error in the make_bem_model function when such overlap occurs (understandably). 

I have tried deleting the bottom slices of the T1.mgz and rerunning the watershed algorithm but that actually made the overlap worse. I have also tried using the -atlas parameter which made it a bit better but not quite (that's actually what is plotted). What I would really like to do at this point is manually edit the surfaces to avoid the overlap which I think given the location and minuscule nature of the overlap. 

Any tips on how to get this done? Or on how to edit the MRI to avoid this overlap to begin with?

Thanks for your help!
Keith
https://dl.dropboxusercontent.com/u/5190414/skulloverlap.png

Inline image 1

Keith Doelling
Dept of Psychology
Center for Neural Science
NYU


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