Not sure why you are getting the holes. There might be WM hypointensties that
would not be captured by your model. I've put a new version of mri_binarize here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_binarize
You can also just use --match ID1 ID2 ... in the mri_binarize that you have
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Original message
From: "Greve, Douglas N.,Ph.D."
Date: 10/10/19 5:56 PM (GMT-06:00)
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] brain mask without CSF ...
You will have to do it manually. You can creat
You will have to do it manually. You can create a binary CSF mask from the
aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST"
not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf).
Then use mri_label2vol to map it into the functional space. Once
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Dear FreeSurfer Experts,
I am running a functional analysis of subcortical structures using FS-FAST
(freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a
brain mask excluding CSF; would it be possible using some option/flag in
