It is technically possible, but you have to set up your own design matrix and contrasts. If you only have two time points, then it will probably be easier to just compute the paired difference and then run the GLM as if it were a single time point

Hello,

we are trying to use covariates while calculating a rmANOVA as described in https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. Is this technically possible with freesurfer?

Thank you, best regards, René

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