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As it has been recommended on FIRST's documentation webpage, we tried FSL vertex analysis using both --useReconNative and --useReconMNI flags along with --useRigidAlign. However, --useReconNative yielded a lot of significant regions on both left thalamus and left pallidum while --useReconMNI yielded none. 

Does this mean that our findings are in fact spurious?

Thanks,

Arash