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Dear FSL experts, In TBSS, I would like to run randomise using gender as a covariate. I'm having some confusion regarding the design.con file and how that needs to be set up. To provide context, I included an example of my design.mat file. This is an example of my current design.mat setup (without all 79 participants included). /NumWaves 4 /NumPoints 79 /PPheights 1 1 /Matrix EV1 (Controls) EV2 (Patients) EV3 (Males) EV4 (Females 1 0 1 0 1 0 1 0 1 0 0 1 1 0 0 1 0 1 0 1 0 1 1 0 0 1 1 0 0 1 0 1 In my design.con file, I currently have: /NumWaves 4 /NumContrasts 2 /PPheights 1 1 /Matrix 1 -1 -1 1 The design.mat and design.con file were created when I first ran TBSS without covariates. I want to now see if my findings hold when I account for gender, so in the design.mat file I added EV3 and EV4 (as shown above). Since the NumWaves is now 4 in the.mat and .con files, I believe I need to have something like this in the design.con file: EV1 EV2 EV3 EV4 1 -1 1 1 -1 1 -1 -1 Would this be the correct way to format the.mat and the .con file to run randomise with two groups and a covariate of gender? My apologies if this has been asked before, but in researching this on the mailing list, the FSL Wiki page on randomise, or tutorials from other labs, I haven't really found a sufficiently clear answer to my question. As always, thank you for your help! Best, Victor