Conventional voxel-based group analysis of functional magnetic resonance imaging (fMRI) data typically requires
warping each subject's brain images onto a common template to create an assumed voxel correspondence. The implicit
assumption is that aligning the anatomical structures would correspondingly align the functional regions of the subjects.
However, due to anatomical and functional inter-subject variability, mis-registration often occurs. Moreover, wholebrain
warping is likely to distort the spatial patterns of activation, which have been shown to be important markers of
task-related activation. To reduce the amount of mis-registration and distortions, warping at the brain region level has
recently been proposed. In this paper, we investigate the effects of both whole-brain and region-level warping on the
spatial patterns of activation statistics within certain regions of interests (ROIs). We have chosen to examine the bilateral
thalami and cerebellar hemispheres during a bulb-squeezing experiment, as these regions are expected to incur taskrelated
activation changes. Furthermore, the appreciable size difference between the thalamus and cerebellum allows for
exploring the effects of warping on various ROI sizes. By applying our recently proposed 3D moment-based invariant
spatial features to characterize the spatial pattern of fMRI activation statistics, we demonstrate that whole-brain warping
generally reduced discriminability of task-related activation differences. Applying the same spatial analysis to ROIs
warped at the region level showed some improvements over whole-brain warping, but warp-free analysis resulted in the
best performance. We hence suggest that spatial analysis of fMRI data that includes spatial warping to a common space
must be interpreted with caution.