open-discussion > RE: Changing default protocol before QC without GUI
Jul 31, 2020  06:07 AM | Martin Styner
RE: Changing default protocol before QC without GUI
Sorry for not being clear:
- the thresholds are specified in the protocol. Using the same protocol means that you apply the same thresholds (which is necessary within a study)
- using "-d" generates a protocol. The thresholds in that protocol are based on the dataset provided when you run "-d" (or when you use the "default protocol" button in the GUI). 
- You don't want to have thresholds computed for every dataset within a single study, but rather use consistent thresholds (i.e. same protocol file)
- the default protocols generate thresholds based on our DWI knowledge back before 2010. My 2020 knowledge tells me that those thresholds are a bit aggressive (particularly for the infant studies that we run) and thus we manually change them to be more permissive.
- There is no need to generate a default protocol, if you have already a protocol. Just load/use that protocol you have.

Re reusing protocol files:
- we do that all the time, if the studies are on a similar level of  SNR (similar acquisitions, similar age range) & motion artifact (similar scanning setting, study population is not expected to impact motion tremendously). 

Additional tips:
- we rarely run the gradient checking step these days(which checks for residual motion that was not corrected in the motion/eddy current correction) as it does not work well on higher shells (and often removes low SNR data in b>2000 shells)
- dominant direction checks needs training data to compute thresholds, and thus is a lot of work on your part. Only needed if you suspect there is an issue with your data (this would be visually evident if you look at the color-FA images). It was a big issue 2005-2010 years, but I rarely see datasets with this issue these days (I think scanner manufacturers solved the problem).

I hope this made things a bit clearer and I did not further sow confusion.

Originally posted by Steven Meisler:
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).

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?


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Steven Meisler Jul 22, 2020
Martin Styner Jul 29, 2020
Steven Meisler Jul 30, 2020
RE: Changing default protocol before QC without GUI
Martin Styner Jul 31, 2020
Steven Meisler Aug 3, 2020
Martin Styner Jul 27, 2020
Steven Meisler Jul 29, 2020