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)


* 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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