Re: [Freesurfer] GM-wm error

Could be a problem with intensity normalization. Are the white matter voxels mostly 110 in the T1.mgz? Also, look at the nu.mgz. I've seen some problems where the nu_correct fails. Usually, this happens when there are a few extremely bright voxels.

doug

Ritobrato Datta wrote:

Hello All,

I ran recon-all for a subject and when I did the following to check the gray matter and white matter segmentation I found that it couldnt do it.

tkmedit subjid brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white

Please see attached fig. All slices are like this one. Can anyone suggest how do I fix it ?

Waiting for your reply

Thank you

Ri

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