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Hi Pavel, Please, see attached an example design. Note that each subject is allocated on its own exchangeability block (EB). - For contrasts C1-C3, use the option "-e design.grp" in randomise. - For contrasts C4-C6, and for the F-test, use the option "-e design.grp" and also the option "--permuteBlocks" in randomise. You may need to split the contrast file (*.con) into two, one with just C1-C3, another with just C4-C6, then make the necessary changes to the *.fts file (F-contrast), and run randomise twice (in separate directories to avoid overwriting results). All the best, Anderson 2015-01-28 14:41 GMT+00:00 Pavel Hok <[log in to unmask]>: > Dear FSL Experts, > > I know that similar questions have been already answered many times, but I > could not find any satisfactory conclusions on the forum. > > I was trying to run 2x3 repeated measures ANOVA (i.e. 3 groups, 2 > timepoints, all subjects have complete data) in FEAT. Since this design is > not mentioned in the GLM manual page, I tried to combine two other designs: > the factors effect approach ( > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_2-factors_2-_.26_3-levels_.282x3_between-subjects_ANOVA.29) > and mixed effects ANOVA ( > http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_2-groups.2C_2-levels_per_subject_.282-way_Mixed_Effect_ANOVA.29 > ). > > Unfortunately, the Feat complains about rank deficiency. Is there a way to > model such a study design? My second guess would be to get the > within-subject contrasts using a FE analysis and then run simple T-test. My > original design matrix is attached. > > Thanks for any ideas! > > Kind regards > > Pavel > > > > -- > > ------------------------------------------------------------------------------- > -- MUDr. Pavel Hok > > ------------------------------------------------------------------------------- > -- Laboratoř funkční magnetické rezonance > -- Neurologická klinika > -- Lékařská fakulta > -- Univerzita Palackého v Olomouci > -- Fakultní nemocnice Olomouc > > ------------------------------------------------------------------------------- > -- Laboratory of functional magnetic resonance imaging > -- Department of Neurology > -- Faculty of Medicine and Dentistry > -- Palacky University Olomouc > -- University Hospital Olomouc > -- Czech Republic > > ------------------------------------------------------------------------------- > -- I.P. Pavlova 6, 775 20 Olomouc > -- web: fmri.upol.cz > -- tel.: +420 588 443 418 > -- e-mail: [log in to unmask] > > ------------------------------------------------------------------------------- >