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Hi Charlie, To run this as a single design on its full generality, with the 3 contrasts (effect of side, effect of time, and interaction), and taking the repeated measures into account (something as a 2x2 ANOVA, with the repeated measures), it'd be necessary a certain permutation strategy that, as of today, isn't available in randomise. However, you can still investigate differences, but you'll need to tweak a bit the pipeline and run randomise 3 times: - To test the effect of side regardless of time: average the two timepoints for each subject (or just sum t1+t2), then subtract L-R, and run randomise with the option -1. - To test the effect of time regardless of side: average each image with itself after flipping (or just sum, L+R), then compute t2-t1, and run randomise with the option -1. - To test the interaction of side and time, compute L-R, then t2-t1, then run randomise with the option -1. To do this, you'll have to take the file all_FA_symmetrised_skeletonised.nii.gz, which is a 4D file, disassemble it (with fslsplit), rename the outputs with meaningful names, e.g. L_subj01_t1.nii.gz, etc, then flip each one (fslswapdim -y) to have the corresponding R_subj01_t1.nii.gz, etc, then compute the sums and differences as above (use fslmaths -add and -sub), then assemble back as 3 new 4D files (fslmerge), and only them run randomise. Note that the file all_FA_skeletonised_left_minus_right.nii.gz already contains the L-R differences, but it's probably simpler to begin and do all starting with the all_FA_symmetrised_skeletonised.nii.gz. For each randomise run you'll have only 4 images in each 4D file, so only 2^4=16 possible sign-flips, which isn't much even for a pilot study. Replacing randomise with a parametric test wouldn't help much either, as you'd have only 3 degrees of freedom per run. I suggest that you try to have more images, even for a pilot. Hope this helps. All the best, Anderson Am 27.01.14 18:24, schrieb charlie Leger: > A few questions regarding tbss_sym FA (pilot project) with a repeated-measures design (within-subjects) 4 subjects (n=4), scanned at two time points; initially and 8 months later. > > The tbss guide suggests using the option -1 for left-right testing in randomise. I don’t think this randomise setting can be used for this project which has two factors: left vs right and time which is a total of 4 levels. This could be set-up as a 2 factor, 2-level Anova (asymmetry: left vs right, time: before and after 8 months), though pairwise test are ultimately needed. > > I did use the glm_gui to attempt make 2-factor, 2-level design (n=4) and can forward it. > > Any suggestions in helping to set up the appropriate design and “randomise” call (e.g. randomise -i all_FA_skeletonised_left_minus_right.nii.gz -o tbss -m mean_FA_symmetrised_skeleton_mask.nii.gz -1 -n 5000 --T2 -V) would be much appreciated. > > Charlie