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First, thank you for the quick reply but I am now confused on the output that I received from fsl_glm. I took your advice (which I appreciate) and entered the following command fsl_glm -i all_FA_skeletonised -d design.mat -o FA_fsl_glm --out_res=Residual My design matrix contained only two EV's, the first one was gender and the second age. I then wanted to test the output to double check that it worked correctly. I therefore reran one of my randomise contrasts without using age or gender as covariates with the new Residual file as the input. The output was completely different than before. So, I was wondering if I used the fsl_glm incorrectly, my logic was incorrect or both. Thanks