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Thanks for the reply Anderson! So should I split up the contrast file so that I have one with the first three and another with remaining contrasts or just run them all together with the two options? Thanks, Tom On Wed, Dec 10, 2014 at 6:16 PM, Anderson M. Winkler <[log in to unmask] > wrote: > Hi Tom, > > Design and contrasts are fine. For the first 3 contrasts, you can use "-e > design.grp" so that permutations will happen only within block. For the > remaining contrasts, use also "--permuteBlocks". > > The groups can be unbalanced, but the number of timepoints need to be the > same for all subjects. > > All the best, > > Anderson > > On 9 December 2014 at 15:51, Thomas Nickson <[log in to unmask]> > wrote: > >> Hi All, >> >> I was looking to do a 3 factor, 2 level repeated measure analysis in >> randomise for some VBM that I am doing and thought that I would run the >> design matrix past the list to make sure that it's okay. >> >> I looked through the list and found this >> >> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1005&L=FSL&D=0&1=FSL&9=A&J=on&K=2&X=190C12580BEC088223&Y=thomas.nickson%40gmail.com&d=No+Match%3BMatch%3BMatches&z=4&P=343446 >> >> and thought that it would be possible to extend it in the following way >> from 2 to 3 factors. >> >> For 6 subjects I get the following design matrix: >> >> Grp G1 G2 G3 s1 s2 s3 s4 s5 s6 >> 1 -1 0 0 1 0 0 0 0 0 >> 2 -1 0 0 0 1 0 0 0 0 >> 3 0 -1 0 0 0 1 0 0 0 >> 4 0 -1 0 0 0 0 1 0 0 >> 5 0 0 -1 0 0 0 0 1 0 >> 6 0 0 -1 0 0 0 0 0 1 >> 1 1 0 0 1 0 0 0 0 0 >> 2 1 0 0 0 1 0 0 0 0 >> 3 0 1 0 0 0 1 0 0 0 >> 4 0 1 0 0 0 0 1 0 0 >> 5 0 0 1 0 0 0 0 1 0 >> 6 0 0 1 0 0 0 0 0 1 >> >> Where, Grp is the group variable, G's are the groups and s is for the >> subject variables. The negative numbers in the group column give T1 and >> non-negative give T2. >> >> Contrasts: >> >> G1 G2 G3 s1 s2 s3 s4 s5 s6 >> 1 0 0 0 0 0 0 0 0 Time2 > Time1 G1 >> 0 1 0 0 0 0 0 0 0 Time2 > Time1 G2 >> 0 0 1 0 0 0 0 0 0 Time2 > Time1 G3 >> -1 1 0 0 0 0 0 0 0 G2>G1 >> -1 0 1 0 0 0 0 0 0 G3>G1 >> 1 -1 0 0 0 0 0 0 0 G1>G2 >> 0 -1 1 0 0 0 0 0 0 G3>G2 >> 1 0 -1 0 0 0 0 0 0 G1>G3 >> 0 1 -1 0 0 0 0 0 0 G2>G3 >> >> Is this correct? >> >> Also, is this only possible in a balanced design where there are equal >> number of people at both time points? >> >> Thanks, >> >> Tom >> >> >> >> >