I’ve noticed two approaches to collecting the water‑reference scan for MRS:
Separate scan: turn water suppression off and run a dedicated reference acquisition.
Integrated scan (Siemens option): enable the “Reference Scan” checkbox so the sequence runs the water reference automatically just before each metabolite block.
Why do many groups still prefer the separate‑scan method? (is it true that many people prefer this?)
If yes, are there technical or workflow advantages that make it the better choice in practice, or is the integrated option equally reliable?
I think the integrated water reference scans are a relatively new feature. My guess is that people like to stick to the protocols they know and have successfully used for years. Maybe more importantly, when using a separate scan, you have full fine control over the details. As an example, you can choose whether you switch off the water suppression module entirely or just deactivate the pulses (the latter is necessary to keep playing out the gradients for optimal eddy-current correction). I’ve found myself wondering when setting up protocols for collaborators what exactly the ‘integrated option’ does here… and decided to set up a classic separate scan just because I wasn’t sure.
In terms of workflow, it’s certainly convenient to have the water reference integrated.
I see. Thank you so much for your reply.
The reason I asked was that I was thinking that for developing the fmri-fmrs pulse sequence whether I should keep the integrated scan option in the sequence or not. If there is not many user, so maybe it is worth taking it out.
It happened to myself that I had to throw away two of my data because I simply forgot to acquire the water ref. But if it was part of the oprotocol, it would have never happened.
Definitely better in terms of workflow.
Honestly, for sequence programming, my instinct is that it’s always easier to leave a feature in rather than to excise it.
Plus, for fMRS acquisitions, there’s added value in acquiring a reference lineshape, especially if that can be done in an interleaved fashion (in that case, you can also use it to update F0).