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Hi, Just wanted to know if I try to see the differences pre and post like Jared asked but looking at regression with a covariable. Do I put this covariable on just one column and do I need to demeaned this variable ? Thank you for your help Arnaud 2014-02-11 7:17 GMT-05:00 Gwenaëlle DOUAUD <[log in to unmask]>: > 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 > > > -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649