I don't think you can. I have not looked at combat in a long time, but I thought they did their own GLM. combat might take a design matrix, in which case you could use mri_glmfit and your FSGD to create the design matrix.
On 8/30/2022 9:37 AM, Rene Seiger wrote:
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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!
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