hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not really possible to diagnose from a single slice from a single subject. If you tar, gzip and upload the subject one of us will take a look

cheers
Bruce
On Thu, 1 Dec 2016, Rizvi, Batool wrote:



Hi FreeSurfer experts,

 

After running -autorecon2 and -autorecon3, we're seeing issues for some of
the subjects, which now start showing changes in intensity/brightness in
some voxels, and this increased intensity is now missed by the white matter
and grey matter segmentation, and is labeled as non-brain matter.

 

 Attached is an example of a subject's brain that was segmented incorrectly,
which we think is due to the intensity around that frontal region. We hadn't
added control points in that region, so we are unsure what the cause of the
intensity change is. In our first pass before running -autorecon2
-autorecon3, we did not notice this error or the intensity values to be so
bright for that region.

 

Thanks for your help!

BR


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