Hi Christine
this looks to me like a consequence of the high myelin content of motor
cortex.If there really is as little contrast there as seems from your
image there is not much you can do except change the acquisition. If you
give us the details we can help with this.
cheers
Bruce
On Thu, 23 Jan 2014, Matt Glasser
wrote:
From: Christine Smith cnsm...@ucsd.edu
Date: Thursday, January 23, 2014 3:58 PM
To: Matt Glasser m...@ma-tea.com
Subject: Re: [Freesurfer] poor grey/white distinction in superior part of
scan
Please note that the left and right sides of the brain are flipped for
freesurfer vs the dicom picture. Please find attached a dicom picture that
is oriented the same way as freesurfer. Sorry for any confusion.
On Thu, Jan 23, 2014 at 1:56 PM, Christine Smith cnsm...@ucsd.edu wrote:
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 m...@ma-tea.com
wrote:
Some pictures would probably be helpful to know what the
issue is.
Peace,
Matt.
From: Christine Smith cnsm...@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
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Christine N. Smith, Ph.D.
Department of Psychiatry
University of California, San Diego
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