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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