I am trying to use randomise to test for a main effect of group in a mixed model design -- patients were scanned at time 1 and time 2, and I would like to test for a main effect of group (patients vs. controls) on resting state functional connectivity (I have tested the group-by-time interaction separately).

The problem seems to be that when I introduce exchangeability blocks, only one permutation is performed -- below is an example using the simplest case with no optional arguments specified (the same problem arises regardless of optional arguments): 

randomise options: -i DMN.nii.gz -o DMN_test -d design.mat -t design.con -e design.grp 

Loading Data: 

Data loaded

1 permutations required for exhaustive test of t-test 1

Doing all 1 unique permutations

And the problem disappears when I don't explicitly specify the exchangeability blocks:

randomise options: -i DMN.nii.gz -o DMN_test -d design.mat -t design.con 

Loading Data: 

Data loaded

1.0907e+20 permutations required for exhaustive test of t-test 1

Doing 5000 random permutations

I'm attaching the mat, con, and grp files.

Thank you for any help!

Best,
Nicole Petersen
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