Thanks, Steve. I don't think that approach will work, since it is describing a between subjects ANOVA, and I am trying to do a repeated measures ANOVA.
I did see this in the manual: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_2-groups.2C_2-levels_per_subject_.282-way_Mixed_Effect_ANOVA.29
but it appears to be describing mixed effects, so I'm not sure if it is appropriate to use, either.
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