I don't know what you mean by " matter and csf signal in my nuisance regressor matrix". It looks like your matrix only has motion and trends. Also, look at this page http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthr...
On 3/25/2020 12:16 PM, Mcnorgan, Christopher wrote:
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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
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- Chris McNorgan
- Assistant Professor
- Department of Psychology
- University at Buffalo,
- The State University of New York
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