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Hi Hamzah, Covariates are added to taken out the variance caused by these covariates. So you can conclude difference in FA between your patient group and control group is not due to age or performance. Example: Your design.mat file: /NumWaves is your column number. /NumPoints is your row number. Below it is a simple example with 3 patients and 3 controls, column 3 is your age (demeaned) column 4 is your response time (demeaned), about if you need to demean, please see the link: http://mumford.fmripower.org/mean_centering/ design.mat /NumWaves 4 /NumPoints 6 /Matrix 1 0 -9.904762 -1.0199608534 1 0 -3.904762 0.4074364068 1 0 1.095238 -1.4254403055 0 1 -1.904762 -1.9898238671 0 1 -6.904762 1.6485322973 0 1 0.095238 0.8786692836 Then, design contrast file: /ContrastName1 "name your contrast" Example: design.con /ContrastName1 "patient_vs_control" /ContrastName2 "control_vs_patient" /NumWaves 4 /NumContrasts 2 /Matrix 1 -1 0 0 -1 1 0 0 Command: randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 see: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide Hope this is helpful to you. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Hamzah Baagil Sent: Tuesday, September 10, 2013 8:45 AM To: [log in to unmask] Subject: [FSL] TBSS covariate Dear FSL experts, I am trying to add a covariate (Age or Reaction time) for my TBSS analysis. In my analysis, I am using a group of patients compare to controls. I have tried using the GLM for the design matrix, but I have difficulties adding covariate to my analysis and interpreting the results. I would be very thankful for any help. Kind Regards, Hamzah Baagil