Dear Daniel,

For the "outer" boundary of your ROI, I would try the betsurf from FSL for the inner skull surface estimation. This should be more precise than using brainmask.mgz.

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide

Antonin

You could remove the brain (as found in aseg.mgz) from the brainmask.mgz. This will leave some dura. It is not an elegant or accurate solution On 03/06/2017 02:24 PM, Albrecht, Daniel S. wrote:

Hello,

We have a PET dataset where we expect to see pathogenic changes in the meninges. We'd like to extract the meningeal signal in subject space, and were hoping to come up with an automated strategy to create meningeal ROIs, containing no brain or scalp. So my question is: can you suggest any way within the FreeSurfer pipeline that we can create a meningeal-only ROI, or alternatively an ROI containing both skull and meninges, but still no scalp or brain?

Your help is greatly appreciated!

Daniel S. Albrecht, PhD Research Fellow in Radiology Martinos Center for Biomedical Imaging