External Email - Use Caution        

I’ve been using mri_glmfit to regress out motion correction parameters and linear trends and saving residuals in surface space by first generating a QA matrix for the volume:

 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:

paste ${source_dir}/${r}/lh.detrend/Xg.dat mcprextreg > nuisance

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

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

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

                                --X nuisance \

                                --no-contrasts-ok --save-yhat --eres-save \

                                --surf ${SURFTOUSE} ${hemi}

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

/**********************************************

* Chris McNorgan

* Assistant Professor

* Department of Psychology

* University at Buffalo, 

* The State University of New York

* http://ccnlab.buffalo.edu/

* Office: 716.645.0236

* Lab: 716.645.0222

**********************************************/

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