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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