[Freesurfer] Covariate for results of cortical parcellation

Hello, Freesurfer experts:

I noticed for analyzing the results from autorecon2, the intracranial volume are controlled as covariate in some publications. Is there any corresponding covariate for cortical results from autorecon3, cortical thickness, surface, and volume?

In my current study, there are two group: one is a group with less optimal developmental environment and the other is control. I noticed that without any covariate, the r square from cortical measure and group variable was really low, only accounting for 2%. Is any standard way to analyze the cortical data?

Thanks!

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