Hi Bruce,
Thanks for your reply. It is actually brighter on the brainmask.mgz than the 
orig.mgz when I checked. I'm uploading the freesurfer subject here.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
Sent: Thursday, December 01, 2016 2:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity 

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

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

Attachment: FTLDES008_FS.tar
Description: FTLDES008_FS.tar

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