Hi Ben,

do the images appear in the right orientation in tkmedit? How did you convert to .mgz? If they are in the correct orientation then feel free to drop an example that isn't working on our website and we'll take a look.

cheers, Bruce On Tue, 28 Apr 2009, Wilson, Benjamin wrote:

Hi,

I am trying to run freesurfer on some SPGR sequences that I have on a few subjects. I managed to import and convert the DICOM files to .mgz with success, but when I ran the skull strip I have a significant amount of skull left in some places and a large chunk of brain missing in other planes on the same brain. I am wondering if there is a problem with intensity normalization (most of my brain appears to be close to an intensity of 110), but I do not know how to fix the problem. Can anybody offer some suggestions on how to fix the problem?

Thanks.

Sincerely, Ben Wilson

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