Definitely the one that leaves stuff around and doesn't strip any brain. Usually that won't be a problem Bruce

On Sep 17, 2012, at 10:20 PM, Skyler Gabriel Shollenbarger shollen2@uwm.edu wrote:

Hello,

After running -autorecon1, there were issues with finding the best water threshold for skull stripping (one value would leave excess anatomy and the next lowest value would leave regions in the cerebellum missing).

FS appears to differentiate brain matter from extraneous anatomy quite well. Do you recommend going with the value that results in remaining anatomy or the value with missing cerebellar regions?

Thanks in advance, Skyler

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Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer