I’ve got a dataset with some consistency problems. Intensity normalized T1s are available for everyone (just the scanner’s intensity normalization) and un-normalized scans are available for ~ 3/4 of sessions. Should I use everyone’s intensity normalized T1s for consistency? Is there a way to signal that a scan has already been normalized? Does freesurfer get passed the intensity normalized output from the segmentation pipeline or do you use the freesurfer intensity normalization? Do you know if the quality of the segmentation or surfaces will be impacted with pre-normalized T1s (as in, is it bad to normalize a scan that’s already been normalized)?
For what it’s worth, this is longitudinal data with somewhere between 1 and 4 sessions per subject.