Dear Matt, 

Please find attached two pictures. One is of the brain from reconstructed dicom files (using AFNI). The other one is a pic from tkmedit of the same subject and approximately the same slice of brain. Notice that the freesurfer image is very bright. Look at the white matter and pial lines (i.e., cortical thickness) in the upper left hand part of the image and see how thin the cortex appears. Notice also, that there is very little grey/white contrast in this same area in the brain image reconstructed from dicoms. 

Please let me know if there are any other pictures you might desire or information you might need. 

Christine

On Thu, Jan 23, 2014 at 11:33 AM, Matt Glasser <matt@ma-tea.com> wrote:

Some pictures would probably be helpful to know what the issue is.

Peace,

Matt.

From: Christine Smith <cnsmith@ucsd.edu>
Date: Thursday, January 23, 2014 1:05 PM
To: <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] poor grey/white distinction in superior part of scan

Hello,

I am emailing to inquire about whether poor grey/white contrast in one part of a scan (i.e., the posterior and superior part of the scan; ~parietal cortex) can be addressed. The contrast in other parts of the scan looks good and freesurfer does a great job of distinguishing white from grey. For the parietal cortex area the cortex appears very thin. In addition, the entire brain appears 'white' or bright, even though the brain doesn't look this bright if you reconstruct it from dicoms. 

We have now obtained 4 scans like this, so it isn't just one person with thinning cortex. 

How can I make an adjustment to only this superior part of the brain and leave the rest of it alone? Or do I need to make an adjustment to the intensity early on for the entire scan and then basically start over with editing? 

Best,

Christine

--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego

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--
Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego