Re: [Freesurfer] How to obtain the CSF mask

There is not a "direct" mask, but you can use mri_binarize --i aparc+aseg.mgz --csf --o csf.mgz

On 5/14/19 12:05 PM, Yaoshen Yuan wrote:

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Dear Freesurfer team,

I am planning to get the CSF binary mask using Freesurfer. I saw previous discussion about combining several labels in aparc+aseg.nii to create the CSF mask. I am now using Freesurfer v6.0.0. I am wondering does FS now offer a direct mask for CSF using recon-all (I saw gm.mask.mgz and wm.mask.mgz under \mri folder ) or do I still need combine different labels to get the CSF mask?

Thank you in advance!

Yaoshen Yuan

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