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I have the same error that doesn't resolve with --mgh or mgz. 

warning: excluding contrast file /Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat since it has multiple rows
ERROR: for surface based analysis, input cannot be nii or nii.gz

Thanks

Stefano