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Thanks Eugene! So how would I use fslmaths at this final stage to determine that RvsG contrast is a positive activation that I am contrasting between groups? I hope this make sense and thanks so much! Eugene Duff wrote: > Hi Vina - > > 2009/5/20 Vina Goghari <[log in to unmask] <mailto:[log in to unmask]>> > > Hi, > I guess this is where I get confused with what to do in my > situation. I have a number of subjects in three groups each - each > subjects three sessions of the same task. > > I have for example 2 regressors (red condition and green > condition), so I set up the analysis for every session and then I > combine across sessions for every subject: > R 1 0 > G 0 1 > RvsG 1 -1 > > Then I want to look at differences between the 3 groups for the > subjects for cope 3 (RvsG): > Group 1 > Group 2&3: 1 1 -2 > Group 1 > Group 2: 1 -1 0 > > Therefore I can't mask the higher level analyses to look at > positive activations at the more basic regressor analyses. > > Am I doing it correctly? And in this case would I use fslmaths to > see if the contrasts of the differences > 0 for the higher level > analysis? > > > Yes, that seems OK (did you make an error writing down the G1 > G2&3 > contrast?). I would probably recommend also looking separately at > differences in R across groups, and the same for G, because with only > your contrasts you won't have any indication whether a change in one > or the other or both is causing any effects in the contrasts of their > differences. Also note that unless groups 2 & 3 have an association > that makes them a natural group, results of the G1 > G2&3 contrasts > will be a bit ambiguous. You won't know whether just one or both of > G2 & G3 is different from G1. > Best, > Eugene > > > > > Thanks! > > > Eugene Duff wrote: > > Hi Vina > > 2009/5/18 Vina Goghari <[log in to unmask] > <mailto:[log in to unmask]> <mailto:[log in to unmask] > <mailto:[log in to unmask]>>> > > Yes that makes complete sense. However, it does not work > for how > I've set up my contrasts and the effects I'm looking for - are > there any other ways? > > I'm not sure how your situation is different? You may be able > to use fslmaths to mask your final thresh_zstat images. > Eugene > > > > Thanks!! > > Eugene Duff wrote: > > If you want to limit you results to regions where, say, the > first regressor was associated with a positive > response, you > can use contrast masking. Select contrast masking in the > post-stats section and input the contrast where you > tested for > a positive response in that condition (e.g. the 1 0 > contrast). > Selecting "Mask using z>0.. " makes the masking less > severe, > showing regions where the fit of the regressor was > positive, > but not necessarily significant. > I hope that makes some sense! > Eugene > > 2009/5/18 Vina Goghari <[log in to unmask] > <mailto:[log in to unmask]> > <mailto:[log in to unmask] <mailto:[log in to unmask]>> > <mailto:[log in to unmask] <mailto:[log in to unmask]> > > <mailto:[log in to unmask] <mailto:[log in to unmask]>>>> > > > Thanks for your response. What is the way to ask for > activations > 0? > > Thanks! > > tEugene Duff wrote: > > Hi Vina, > > 2009/5/18 Vina Goghari <[log in to unmask] > <mailto:[log in to unmask]> > <mailto:[log in to unmask] <mailto:[log in to unmask]>> > <mailto:[log in to unmask] > <mailto:[log in to unmask]> <mailto:[log in to unmask] > <mailto:[log in to unmask]>>> > <mailto:[log in to unmask] <mailto:[log in to unmask]> > <mailto:[log in to unmask] <mailto:[log in to unmask]>> > > <mailto:[log in to unmask] > <mailto:[log in to unmask]> <mailto:[log in to unmask] > <mailto:[log in to unmask]>>>>> > > > > Hi, > A couple of quick questions about when setting up > contrasts: > > (1) If you have two regressors that at a > lower level you > set up: > R1 0 1 > R2 1 0 > > And then you contrast: -1 1. Do you still > have to be > worried that > the contrast could stem from a difference > that is below > zero for > both regressors? > > If I understand you correctly, then yes, this > contrasts > would > identify differences in responses even if they > are all > negative responses (deactivations). (2) > When you have three groups can you set up your higher level > contrast this way to sum 0 (1 1 -2)? > > This contrast will find regions where the responses > modelled > by the first two evs are significantly greater > than those > modelled by the third EV. These regions may not > necessarily > remain signficant when only one of the first two > evs is > contrasted with the third. > Best > Eugene > Thanks! > > > > > -- > Eugene Duff > > FMRIB Centre, > University of Oxford > John Radcliffe Hospital, Headington OX3 9DU > Oxford UK > > Ph: +44 (0) 1865 222 739 Fax: +44 (0) 1865 222 717 > > -- > > > > > -- > Eugene Duff > > FMRIB Centre, > University of Oxford > John Radcliffe Hospital, Headington OX3 9DU Oxford UK > > Ph: +44 (0) 1865 222 739 Fax: +44 (0) 1865 222 717 > > -- > > > > > -- > > Eugene Duff > > FMRIB Centre, > University of Oxford > John Radcliffe Hospital, Headington OX3 9DU Oxford UK > > Ph: +44 (0) 1865 222 739 Fax: +44 (0) 1865 222 717 > > -- > > > > > -- > > Eugene Duff > > FMRIB Centre, > University of Oxford > John Radcliffe Hospital, Headington OX3 9DU Oxford UK > > Ph: +44 (0) 1865 222 739 Fax: +44 (0) 1865 222 717 > > --