Hi James
It really depends on your sequence. Some sequences, like mprage, trade off SNR for CNR, so the distance between gray and white is larger, but the noise in each is also larger. In that case white might end up brighter because of the noise. There are also inflow effects where you get non-inverted spins coming in through arteries that are very bright in mprage, that you won’t see in a flash scan. We don’t actually set the gm peak, just scale the white to 110-ish, then gray lands wherever the intrinsic contrast of the image puts it
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of James Brown Sent: Saturday, October 22, 2022 10:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_segment
External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flags "-whi" and "-ghi" in the command "mri_segement". According to FS wiki, the command "mri_normalize" sets white matter voxels around ~110 and gray matter around ~70. - The default white matter high limit in the command mri_segemnt is 125, what is the highest value to consider white matter voxels in an image? Is it 125? - What are the situations where we need to set the gray and white matter voxels at a high limit of 100 and 125 respectively in the command mri_segment? Does the brightness of the image or motion play a role in the decision of choosing high limits values?
Thank you, James