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You can try
mri_binarize --i aseg.mgz --csf --o csf.mgz
to get a binary map
Note that the aseg does not have sulcal CSF labeled. But you can get that with something like
samseg --i orig.mgz --o samseg
Then run mri_binarize on the seg.mgz file

On 8/27/2023 3:05 AM, Michael Mc Laughlin wrote:

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Hi,

recon-all does not seem to produce a map of CSF. My research is especially interested in how CSF is distributed. Is there a way to get this?

Michael McLaughlin,
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