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Hi Amir

The brain.mgz isn’t used for subcortical segmentation so this may not matter. Check the aseg.mgz over the norm.mgz and see if it retrains the contrast and has the correct boundaries. The intensity normalization in the brain.mgz is much more aggressive, although it can be turned down if your sequence doesn’t have enough CNR in some regions

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of AmirHussein Abdolalizadeh Sent: Thursday, July 13, 2023 7:25 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Basal Ganglia in brain.mgz denoted as WM

External Email - Use Caution Hi Freesurfer users/experts,

I accidentally noticed a bizarre behavior -in my opinion- in the FreeSurfer 7.3.2 in which there were large regions of the basal ganglia changed to the WM value (value = 110). Both the original T1 and the brain.mgz screenshots are attached. I haven't tried it with the latest FreeSurfer versions but it seems quite odd.

Any comments are appreciated.

Best, Amir