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