[Mne_analysis] Trouble with mne_watershed_bem

Stephen Politzer-Ahles politzerahless at gmail.com
Sat Feb 4 14:41:16 EST 2012
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Hi MNEers,

I am using mne_watershed_bem to create boundary element models (my MRI data
do  not seem to be in the right format to use FLASH images or seglab, and
so far I haven't had much luck getting it done in BrainSuite); the results
for the brain surface and inner skull look good, but the results for the
outer skull and outer skin do not (that is to say, those boundaries go way
off the top of the head, making what looks like a mushroom above the head).
However, my functional data is all MEG data (I'm not planning on doing any
source localization of EEG data), and my understanding of the materials
I've looked at is that MEG solutions just need the inner skull; thus, would
it be ok for me to go ahead with poor segmentations of the outer skull and
scalp?

Also, if it turns out I do need the outer skull and scalp, are there any
options in mne_watershed_bem that I can use to improve the segmentation?
I've tried running it both with and without --atlas, but I only saw a
little bit of improvement. I noticed that the corresponding Freesurfer
routine, http://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed, has many
parameters that can be specified, but I don't know which of these (if any)
might improve the segmentation.

Thanks,
Steve Politzer-Ahles

-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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