RE: Are white matter and CSF confounds saved as files?

Thanks for the recommendation, Alfonso. I was able to run the code. It looks to have created a series of .txt files for each run per subject with the prefix "dp_" as you said.

One question about the white matter and CSF regressors, should I construct the regressors from the fully preprocessed files (i.e. after smoothing, normalization, and realignment)? The full name of the output files is "dp_swuepi_run1.nii" so I wanted to make sure that this was the correct order to run the pipeline.

Thanks,
Matt