Dear FSL list,
I am running a TBSS study with 2 groups of subjects (1 vs 2). Each group has a within-subjects factor of two levels (A vs B). I would like to be able to test the main effects of group and condition separately, and more importantly to examine the group by condition interaction.
I have a design matrix in which the groups are specified by “1” and “2” in design.grp, the within-subjects factor are modelled in separate EVs, and the repeated measures specified by subject-specific EVs. There are also demeaned covariates of interest (Cov1, Cov2 etc). My design matrix therefore looks like:
Group 1A 1B 2A 2B Cov1 Cov2 Subj1 Subj2 Subj3 Subj4
1 1 0 0 0 -3 0 1 0 0 0
1 0 1 0 0 -3 0 1 0 0 0
1 1 0 0 0 2 0 0 1 0 0
1 0 1 0 0 2 0 0 1 0 0
...etc
2 0 0 1 0 0 4 0 0 1 0
2 0 0 0 1 0 4 0 0 1 0
2 0 0 1 0 0 -1 0 0 0 1
2 0 0 0 1 0 -1 0 0 0 1
...etc
I have called the design in randomise as follows:
randomise –i all_FA_skeletonised.nii.gz –o FA –d design.mat –t design.con –m mean_FA_skeleton_mask.nii.gz –D –T2 –V
However, after the first permutation, this message is generated:
1.83449e+25 permutations required for exhaustive test of t-test1
Doing 5000 random permutations
Starting permutation 1 (Unpermuted data)
Starting permutation 2
Warning: tfce has detected a large number of integral steps. This operation may require a great deal of time to complete.
The permutations then stall and progress no further. Looking at previous posts on this message, others have found that it can be generated by corrupted data (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;b0af05ef.1010) or “an error in the design matrix” (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;e8b434e6.1008). Our data is not corrupted. In addition, we have found that randomise runs perfectly well if we do not include subject specific EVs. We have applied a similar design matrix to a voxel-based analysis of the data in SPM, and there are no such problems.
(1) My first question is: would FSL users be able to confirm that this is an appropriate way to specify a repeated measures design in a TBSS design matrix?
(2) Secondly: why does introducing subject-specific EVs modelling repeated measures generate this integral steps message? What action can I take to solve it?
Many thanks,
Charlotte
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