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Dr. Smith, Do you mean by using fsl_glm for dti data. For example, I have one group of subjects (8 boys v.s. 8 girls) who had annual DTI exam. I have 2-year data. I used 2-factors 2-levels ANOVA design matrix. Fixed effect: gender, age (year) only one year difference, interaction between the two. I used the following command for the randomise. $ randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -e design.grp -f design.fts --T2 -V Instead of the above command, we can use: fsl_glm -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -e design.grp -f design.fts What do you mean by output COPEs? Thanks yingying >>> Stephen Smith <[log in to unmask]> 10/6/2011 2:46 PM >>> Hi - you can use fsl_glm and tell it to output COPEs…. Cheers On 6 Oct 2011, at 17:35, Arnold Evia wrote: Hello, I am an undergraduate student using TBSS for research. I have been using TBSS, and getting great results. However, when it comes to statistical analysis using randomise, is there a way to find the estimated parameters after permutations? The estimated parameters that I am referring to are the parameters in the general linear model. Y=XB+n, where X is the design matrix input and B is the matrix of estimated parameters (the information I am looking for). Thanks in advance, Arnold Evia --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------