mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \

                        --glmdir ${source_dir}/${r}/{hemi}.detrend \

                        --qa \

                        --surf ${SURFTOUSE} lh

Then merging the QA and MC matrices into a single matrix of nuisance regressors:

And finally, regressing out the nuisance values and saving the residuals

Is there a straightforward way of obtaining mean white matter and csf signal in my nuisance regressor matrix? I was unable to find any preprocessing step or application of mri_glmfit that will provide these values or regress out these values automatically. 

(Also note: the —qa flag is not documented in the mri_glmfit help; I must’ve learned of it from a previous email to this list)

Thanks