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 Graduate Student Behavioral and Brain Sciences Program Psychology Department 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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Hi Jordan

sorry, this one slipped through the cracks. There really is no way except visual inspection, and thalamus is particularly hard. You need to play with the brightness/contrast to really see the lateral borders, and even then it can be difficult depending on your acquisition.

cheers Bruce

On Wed, 8 Aug 2012, Jordan Pierce wrote:

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

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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

  <40211_noaseg.PNG>

  <40211_aseg.PNG>

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.