the brainmask is essentially a binary mask. YOu should use the brain.mgz not the brainmask for cortical stuff. For subcortical segmentations you should overlay the norm as it is the input to the aseg. The brain volume will have these borders eroded as it is only used for cortical surfaces not for the aseg
cheers Bruce
On Mon, 2 Oct 2017, Jeff Crawford wrote:
Perfect! I looked at the norm.mgz and each of the subcortical regions was perfectly represented and matched the segmentation. What did you mean by "don't loom at the aseg on top of the brain mask?" I thought it was appropriate, because I am doing pial corrections and the online tutorial said I needed to use the brainmask.mgz. What is the difference between norm.mgz and brainmask.mgz in this case?
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, September 30, 2017 9:33 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Can someone tell me why my subcorticals look like this?
Hi Jeffrey
I’m not sure I understand. By default we will resample to 256^3 and 1mm iso, but that shouldn’t stretch anything. And don’t loom at the aseg on top of the brainmask. Look at it on the norm and you should see pallidum, putamen and thalamus. Cheers Bruce
On Sep 29, 2017, at 9:35 AM, Jeff Crawford jcrawf29@jhmi.edu wrote:
Jeffrey
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