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Dear Greg, yes, my intent is to regress motion parameters from the timeseries before running FIX. At the moment I am working with long rs-fMRI scans (2000-4000 scans) and I have the problem that the MELODIC would not converge into a finite number of component when using the automatic algorithm for component selection. Therefore I am now trying to do some pre-processing before running ICA-artifact removal using e.g. FIX. It actually works well if I do an initial MELODIC, setting a limited number of components myself, and thereafter apply FIX with threshold 0 and the option -m. Then I run a second melodic, and this time the component number converges automatically to a certain number, and based on those I can use FIX to remove the other artefacts (eg. CSF or white matter, scanner artifacts, vascular related, ...). However I was looking for a "smarter" and faster way to do the same motion regression script without running two melodic. Another thing I noticed is that motion-related components are present also in neural components (visible also in the spectra), so if I regress the motion beforehand, the actual component is "cleaner" and easier to distinguish. Best, Valerio ____________________ From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Greg Burgess [[log in to unmask]] Sent: Tuesday, February 16, 2016 5:26 PM To: [log in to unmask] Subject: Re: [FSL] FIX and Motion Regression Hi Valerio, Can you explain a bit more what you're trying to accomplish? Are you trying to regress motion parameters from the timeseries BEFORE running FIX? As you say in your original email, "I believe that motion is a strong confound in the analysis and in the scoring of the components into good or bad." Given that signal related to motion is a strong factor in the ability of the FIX classifier to distinguish good and bad components, are you sure that you want to risk affecting the performance of the FIX classifier by removing those motion-related signals? --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Neuroscience Phone: 314-362-7864 Email: [log in to unmask]