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Dear expert, I am working on a resting state fMRI pipeline. I have performed several preprocessing steps (e.g. trimming, despiking, etc.) and now I want to get performed fsl_glm and regress out nuisance regressors (WM, CSF signal, and motion). In order to do that I ve run the following command fsl_glm -i filtered_func_data.nii.gz -d design_with_nuisance.mat —out_res=filtered_func_data_new.nii.gz The filtered_func_data_new.nii.gz are the residuals of the model that has these variables, hence will be free of these nuisance effects. As for the design_with_nuisance.mat I’ve merged together the .par out from mcflirt (mcflirt -in func.nii.gz -mats -plots -meanvol) with the CSF.txt and WM.txt timeseries. So the final mat files has 8 columns (6 for the motion parameters and 2 for CSF and WM). However the final filtered_func_data_new.nii.gz is really weird and far away to be a cleaned rsfmri. I was wondering whether if I am doing something wrong… As I was wondering how can I include the confound.txt output of fsl_motion_outliers (fsl_motion_outliers -i rsFmri_trimmed_despike_mcf_tshift.nii.gz -o confound.txt --fd --thresh=0.25 -p fd_plot -v > outlier_output.txt)?? Thanks for your help Best Dave ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1