We ran our preprocessing using the default intermediate QC/ART settings, which resulted in QC second-level covariates from the 5z/0.7mm ART thresholds.  Needing to be a bit more conservative with ART thresholding, we reran the preprocessing routine using the conservative ART settings, which did update the masks and regressor files.  However, how do we generate a new set of QC metrics in the second-level covariate section to reflect the more conservative ART settings (i.e., QC_valid_scans for new ART threshold results)?  Rerunning the preprocessing pipeline does not automatically generate a new set of QC second-level variables.

Thanks,
Jeff