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Hello, the prewhitened data output will not have the confound matrix removed, the residuals ( res4D ) will contain the prewhitened, de-confounded data with the mean removed, if you add the original mean back ( generated with e.g. the -Tmean option in fslmaths ) then this will be your fully processed data. Hope this helps, Kind Regards Matthew -------------------------------- Dr Matthew Webster FMRIB Centre John Radcliffe Hospital University of Oxford On 25 Aug 2018, at 18:48, Dmitrii Paniukov <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello all, I want to prewhiten my fMRI data and regress out a confound file. Will this command do the job? film_gls --in=filtered_func_data.nii.gz --outputPWdata --pd=confound1.mat Thanks! Dmitrii ________________________________ To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1