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For computational purposes, it should be sufficient to simply drop
the last of the 3 input datasets to 3dDeconvolve. If it then whines
about having extra stimuli, you might have to apply -GOFORIT.
If you are only giving 1 dataset (of 3 runs) to 3dDeconvolve (and
are therefore using -concat), use 3dTcat to remove that last run.