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
On 5/22/2019 10:19 AM, Barletta, Valeria wrote:
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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