[Freesurfer] Vertex-wise analysis using ComBat

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Dear FreeSurfer community!

We collected structural data from different scanners and we want to conduct a surface-based (vertex-wise) analysis in FreeSurfer using predefined regions of interest. The model is quite simple, as we just want to correlate a specific (e.g. behavioral) measurement from all subjects (one group) with the thickness on the surface in specific ROIs. To account for the different scanner types, we are planning to use ComBat to account for this effect. However, we are not quite sure how and at which stage we could implement ComBat using the standard FreeSurfer FSGD file approach. Any help would be highly appreciated, Thanks!