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Hi Jared, just a quick tip: while your design is correct, one very simple design to do the same thing would be to take the TBSS (or VBM for that matter) difference between pre and post for each subject and then simply set up a two-tailed t-test (then no need for a design.grp and complex design.mat/con). This is also what we recommend doing in randomise when you have more than one group and 2 timepoints. Cheers, Gwenaëlle ------------------------------------------------------------------------------------------------------------------------ Gwenaëlle Douaud, PhD University Research Lecturer & MRC Career Development Fellow FMRIB Centre, University of Oxford John Radcliffe Hospital, Headington OX3 9DU Oxford UK Switchboard: +44 (0) 1865 222 493 Fax: +44 (0) 1865 222 717 www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud www.fmrib.ox.ac.uk/research/fmrib-interface-analysis-clinical-neuroscience-group ----------------------------------------------------------------------------------------------------------------------- ________________________________ De : Jared Tanner <[log in to unmask]> À : [log in to unmask] Envoyé le : Lundi 10 février 2014 20h35 Objet : [FSL] Longitudinal MRI TBSS matrix design Hi FSL team, I wanted to verify that I had correctly set up matrices and contrasts for a 2 time point longitudinal MRI (10 subjects, repeated once). I used glm_gui to create the design, hopefully as a paired t-test. design.mat /NumWaves 11 /NumPoints 20 /PPheights 2.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 /Matrix 1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 -1.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 design.con /ContrastName1 condition Pre > Post /ContrastName2 condition Post > Pre /NumWaves 11 /NumContrasts 2 /PPheights 2.000000e+00 2.000000e+00 /RequiredEffect 4.414 4.414 /Matrix 1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 -1.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 design.grp /NumWaves 1 /NumPoints 20 /Matrix 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 The randomize command I ran was: randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -e design.grp --T2 Does this design and this randomise command seem accurate? Thank you for any help anyone can provide, Jared Tanner