That is a great solution, thank you!

How exactly can I apply this whole thing to .mgh surface-based files? 

I cannot convert them to .nii and I think mri_binarize and mri_segstats work only on volumes.

Thanks,

Vale

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Wednesday, May 22, 2019 10:47:19 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] question on surface analysis

Dear Freesurfer,

I have a surface file containing values of a cortical myelination index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh)

What I need to do is:

- Masking the surface file with the lesion mask, to create a new lesion mask that contains the myelination index values from rh.MS075_CME.mgh;

Try
mri_mask rh.MS075_CME.mgh rh.surf_CL03.mgh  rh.MS075_CME.mask.mgh

- Assess the percentage (or also the absolute number) of vertices that are under a certain threshold of myelination index values whithin the new lesion mask.

You can use mri_binarize to create a mask of the myelination map (use --min and --max to spec the range), then use mri_segstats inputing the binarized mask with --seg and using --id 1. In the output summary file (--sum sumfile), the "number of voxels" will be the number of vertices; this could be modified to give the surface area instead.

What is the best way to do this?

Thank you,

Vale

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