If thresholds are determined upon running DTIPrep and not generating the protocol, does that mean if I have several studies I want to do QC for, that I can use a single protocol.xml file? I would turn off the image and diffusion bchecks since that would likely fail if I use a study that has different acquisition parameters than the .nrrd I use to generate the original .xml.

My main goal is to only run baseline averaging, and the automated gradient removal steps (slicewise, interlace, gradient, dominant direction).

*Edit*
I have since tried to use a protocol from one study on another, and it didn't look like relevant thresholds (like interlace correlation threshold) were updated.

I cannot seem to create a default protocol without loading a subject first, so to me it seems like it would cause all thresholds for the study to be set for that subject it I were to only use the one protocol.

Is there either 1) a method of loading all subjects to DTIPrep and then generating a protocol so the thresholds are appropriate for the whole cohort, or 2) a way to have DTIPrep calculate these thresholds upon execution as opposed to reading from the protocol? Or am I thinking about this the wrong way?

Thanks,
Steven