Hello,
I am currently following this outline (https://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt1/index.html) to conduct tbss from a set of data consisting of 2 groups of 4 subjects with 2 visits a piece (16 total). I am currently in the process of creating my design matrix based on the ANOVA: 2-groups, 2-levels per subject (2-way Mixed Effect ANOVA) from this webpage: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#ANOVA:_2-groups.2C_2-levels_per_subject_.282-way_Mixed_Effect_ANOVA.29
I think I have successfully created my design.con from the previous link, however, the last portion says fslmaths is required rather than randomise. I am unsure how to subtract the visit images after all of the data has been skeletonised. Which version of the FA maps would I use for fslmaths? (ex. there is FA_to_target, FA_to_target_warp).
In short, I have the design matrix and skeletonised FA, but am unsure how to run statistics using fslmaths. Any help would be appreciated. Thanks!
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