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Hi Christian, I have tried to use MELODIC to get the noise components, and then use these noise components as EVs, as you suggested in the mail archive. I'm afraid some things are not completely clear to me: - You suggested to use first the noise regressors in the model, and then the regressors of interest. I do not understand why the order of EVs would make a difference? - I have tried it with 10 noise EVs, and 1 EV of interest (EV11, which is a simple square wave). EV11 was orthogonalized to the first 10 EVs. Further, for the 10 noise EVs I turned off convolution, temporal filtering and temporal derivative. Then I got my design matrix with a very odd looking EV11, caused by the orthogonalization (I think): the square wave could no longer be recognized. The contrast I was interested in was (0 0 0 0 0 0 0 0 0 0 1) So far so good I hope. The results I got however were less significant than when analyzing with only the square wave (no noise regressors): z-scores dropped (for example the highest z-score dropped from 14 to 12). Do you think my approach is correct? If so, isn't it surprising to see effects of interest become less significant with 11 Evs, of which 10 explain noise? Thanks a lot, Serge. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Stephen Smith Sent: Monday, May 05, 2003 6:47 PM To: [log in to unmask] Subject: Re: [FSL] preprocessing in feat and melodic Hi Jack, On Mon, 5 May 2003, Jack Grinband wrote: > >..."intensity normalisation", which also > >includes a simple thresholding step as well. you won't be getting > >this step in 3a and 3b, so that probably explains things. > > Is this a thresholding for extreme values? no, it zeros values below a lowish threshold to remove background voxels from further calculation. > I often get ICs that are clearly motion artifacts. Since melodic > performs motion correction before doing ICA, I assume that these > components are due to the non- linear effects of motion. Presumably, > any linear effects would be removed by mcflirt. Is that right? that's pretty much it, yes. by "linear" you mean here "rigid body". residual effects could be also be slight inaccuracies in the motion estimation / interpolation artefacts (similar thing), or physics effects such as "spin-history". > I am interested in removing some of these components from my FEAT > analysis. If I create regressors of no interest, it seems to me that > I am reducing the power of my regressors of interest. Christian had > mentioned in a previous message that it's possible to make a 4D > representation of the noise and subtract it out. How can I do that? you can do that with the -f option - if it's not already in the email archive, Christian can mayb expand slightly on that. Thanks, Steve. Stephen M. Smith MA DPhil CEng MIEE Associate Director, FMRIB and Analysis Research Coordinator Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve