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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