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Hi Vasilisa, Seems like you made a small mistake by creating the first column in the design matrix. The one that has 0 0 0 1 1 1 . . . This makes a total of 5 waves, instead of 4. Remove the first column and it should be fine! The error shows up because of a mismatch between the design matrix and the contrast matrix. The contrast matrix expects 4 waves (as defined in the design /NumWaves 4). Regards, Stijn Michielse Research Assistant Dept. Psychiatry and Neuropsychology Maastricht University E-mail: [log in to unmask] **************************************************************************** Dear FSL users, I try to set up a randomise 2-group design with two covariates (one continuous one categorical) but I'm keeping to receive the same error. My design matrix : /NumWaves 4 /NumPoints 33 /PPheights 1 1 1 1 /Matrix EV1 EV2 EV3 (gender) EV4 0 1 1 demeaned cov4 0 1 -1 demeaned cov4 0 1 1 demeaned cov4 1 0 -1demeaned cov4 1 0 -1 demeaned cov4 1 0 1 demeaned cov4 . . . my design.con are: /NumWaves 4 /NumContrasts 4 /PPheights 1 1 1 1 /Matrix 1 -1 0 0 -1 1 0 0 0 0 0 1 0 0 0 -1 the randomise command is : randomise options: -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 500 --T2 -V The error: Loading Data: Data loaded ERROR: Program failed An exception has been thrown Runtime error:- detected by Newmat: process fails to converge MatrixType = Rect # Rows = 33; # Cols = 3 Trace: SVD; pinv. Exiting It seems that it does not process all the 4 columns of the design... Does it look like some text:syntax error or something is conceptually wrong? I tried to set up the matrix via GLM gui but the error persists. I also tried to run it with the non-demeaned covariate since Jeannette's recent guideline explains that I probably do not need mean centering as I'm not interested in the individual group means. I also tried to run it with the demeaned data but it is the same error. I recently ran a similar design on Mac with the same version of FSL 4.1.7 and it seemed to work. Now I'm working on Linux machine. would greatly appreciate any comments and prompts. Vasilisa.