I mean to tar and gzip the entire subject dir, which will be too big to 
email. You can put it on our ftp site:


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

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