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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Are there ANY similarities between the two results?
I would expect the default level of refinement in 3dQwarp to produce decent results in the center of the brain, but not so much in the periphery of the cortex. Running the program with the options
-pblur -minpatch 9
(that is, to the finest level of matching) might work better. Of course, it will be slower.