Hi Bruce,

The nu.mgz volume is has the most pronounced contrast between grey and white matter. The orig.mgz volume blurs the distinction between white/grey matter to a point where it is difficult to tell by visually inspecting it.
The grey matter in the orig.mgz volume has values as high as 147-155 while the grey matter in the nu.mgz volume is 95-101 on average.
Regardless the surface or white matter boundaries do not extend to where my control points are placed. I will attach a shot of these volumes if it necessary.

Thank you for your help.
Gonzalo


On Wed, May 8, 2013 at 11:06 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Gonzalo

it's hard to tell from just that image. What does it look like before normalization (e.g. the nu.mgz or orig.mgz)? Is there gray/white contrast there?

cheers
Bruce


On Wed, 8 May 2013, Gonzalo Iribarne wrote:

Hello Freesurfers,
There are some areas of grey and white matter that are rendered with similar brainmask values ranging from 100
- 122 for some of my participants. I have added control points in order to identify which voxels are white
matter, but they are excluded from wm.mgz, as well as the white and grey matter boundaries.
Is this a normalization error? Are the motion artifacts visible in the T1 a factor?

-Gonzalo

Inline image 1




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