There is not one file for CSF or GM, but you can extract them from other files. Eg, mri_binarize --i aparc+aseg.mgz --ventricles --o ventricles.mgz mri_binarize --i aparc+aseg.mgz --gm --o gm.mgz You can use aparc+aseg.mgz as your brain mask

On 5/25/2021 6:14 PM, Camargo, Aldo wrote:

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Hi Freesurfer experts:

I used recon-all all to in my MPRAGE image and I would like to know which file is the corresponding to the CSF (cerebral spinal fluid).

Also, which is the correct file to choose for the brain extracted image, because I see 2 files that can be:  T1.mgz, brain.mgz , which one is the correct ?

Also for GM the file is aparc+aseg.mgz the correct file ?

Thanks a lot and have a nice day,

Aldo

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