When using the norm.mgz, what is the best way to evaluate the accuracy of the thalamus labeling? If lateral thalamus has low contrast with WM, how can we tell where its borders should be? Or is it best to assume that the automatic segmentation has done sufficiently well?
 
Jordan Pierce
The University of Georgia
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: Jordan Pierce <jepierce87@yahoo.com>
Cc: Freesurfer Support <freesurfer@nmr.mgh.harvard.edu>
Sent: Monday, July 23, 2012 1:25 PM
Subject: Re: [Freesurfer] Subcortical segmentations

Hi Jordan
Don't try to evaluate the accuracy of the thalamus label on the brain.mgz, use the norm instead. Lateral thalamus is heavily myelinated and many segmentations miss it since its contrast with the wm is low

Cheers
Bruce



On Jul 23, 2012, at 11:34 AM, Jordan Pierce <jepierce87@yahoo.com> wrote:

Hi,

I have a question about subcortical segmentations: there are a lot of places across subjects where the thalamus label seems to include white matter (images attached), am I right to think that this needs to corrected and is there any reason the program might do this so often?

Thanks,
 
Jordan Pierce
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