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Hi On Tuesday, Oct 28, 2003, at 13:14 Europe/London, Johanna Pekkola wrote: > Dear FSL people, > > I am having problems to understand a contrasting & design matrix > question. > > My experiment is basic: a block design with one active condition and > a baseline. I have run the GLM-analyses by having one EV (EV1, for the > active condition) and one contrast with value 1 for EV 1. So, the > resulting statistical maps show the regions where voxels time-courses > follow the model in the specified level of signifigance. These areas > are > then considered "activated". > That sound right > Iīve read articles where baseline > active condition contrast is > represented (in addition of active condition > baseline contrast), with > same kind of block design. How is this done? > I canīt feed in both EV 1 and baseline in the design matrix and have a > 1 -1 > contrast since the two EVs would be a linear combination of each other. There is a difference between multiple EV's and multiple contrast. With multiple EV's you have to make sure that the design matrix is not rank deficient (i.e. one of the EVs is a linear combination of the other ones - this will make the model unidentifiable) You can, however, have as many contrasts as you wish (contrasts are used to combine beta estimates - i.e. they can't interfere with the estimation anymore). In your case, the design only contains your single EV1 and a contrast of 1 asks for regions in the brain where 'activation>baseline'. A contrast of -1 asks for 'baseline > activation'. There are more details at http://www.fmrib.ox.ac.uk/fslcourse/fmri/s_2722_con.htm or in chapter 14 of 'Functional MRI - an introduction to methods' ta christian > Could I use orthogonalizing of the contrasts? Or is this kind of > thinking at all sensible since I do not have a baseline for the > baseline? > And what would be represented if I ran the EV 1 contrast with value -1 > instead of 1? > > Sorry for these stupid questions... > And thanks for help the previous times. > > Best wishes, > Johanna Pekkola > TKK/LCE > Espoo, Finland