You will need to create your own design matrix that includes both the "QA" terms (which I think are just a constant, linear, and quadradic terms) and your motion regressors. The QA terms you can see in the Xg.dat file. Once you have a design matrix (in simple text/ascii format), you can pass it with --X. You can add --no-contrasts-ok so that it does not complain that you did not specify a contrast.
On 7/10/2019 9:24 PM, Mcnorgan, Christopher wrote: Hello FreeSurfers,
I have an existing pipeline that computes the residualized time series after removing any linear trends using mri_glmfit:
mri_glmfit --y ${source_dir}/${r}/${filepat}.${surf}.${hemi}.nii.gz \ --glmdir ${source_dir}/${r}/${hemi}.detrend \ --qa --save-yhat --eres-save \ --surf ${SURFTOUSE} ${hemi}
This saves the detrended eres.mgh data in *h.detrend/ I would like to additionally include motion correction values as regressors in this step, but I am not completely clear how to do this. My best guess is that this will entail a fixed effects analysis using the values in mcprextreg, but I cannot find any examples of this in the mailing list archives nor on the wiki, so any help would be greatly appreciated!
Thanks, Chris
/********************************************** * 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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