Use mri_glmfit with the --pvr option. You would use one of the modes as the input (--y) and one of the modes as the per-voxel regressor (--pvr). When you make a contrast, you need to include elements for each PVR (the PVR forms a vertex-specific regressor in the design matrix)
doug

On 8/31/14 5:42 AM, Martin Scherr wrote:

Dear Freesurfer-community,

here is a question from a Freesurfer newbie.

I am trying to correlate vertex measures of function (z) and structure (cortical thickness) vertex wise in the individual subject space of one patient.

What would be a good tool for this?

Best,

Martin
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