Add acquisition documentation

[emdupre]

.@dowdlelt had compiled a google spreadsheet of published multi-echo scanning parameters. It would be great to include this in a more general, motivating section of the readthedocs on what mutli-echo EPI acquisition entails, such as echo times, effective echo spacing, in-plane acceleration, etc.

I think that @dowdlelt is getting started on this ! If there's anything else that could / should be added, it'd be great to keep track of it here.

This is done, now ! 🎉 ✨

Following our May tedana developers calls, @jbteves came up with the following actionables:

• link datasets and their sequence parameters (fixed by Update multi-echo.rst #284)
• add parameter adjustment locations for various scanner manufacturers
• link to CMRR for guidance on getting sequences at institutions

I think @handwerkerd @dowdlelt and @tsalo (currently) have the most expertise on this, but it would of course be great to get feedback from anyone interested in acquiring multi-echo data !

[dowdlelt]

Strong motivation to make some progress here - I've nearly finished adding details to what is on the spreadsheet - but I'm quite certain I am still missing some papers. I'm not strong with the idea of adding to the documentation, but I'm still motivated to figure it out. I'll keep chipping away at it - for delays, please blame the world cup. Thanks for the shout out

[tsalo]

To consolidate discussion from Gitter, here are some recommendations for doing multi-echo with the CMRR MB sequence. They are Siemens-specific (and maybe even 3T-specific as well), but may be useful generally. We want to consolidate recommendations for each sequence and scanner into cohesive sections, pages, or even just paragraphs, as well as to share protocol PDFs for basic versions of these sequences to make replication and adaptation easier.

• Number and timing of echoes can be set in "Contrasts" in Sequence, Part 1 tab.
• If you want short TEs and are using GRAPPA acceleration, use an excitation pulse of 4000-4200 and enable LeakBlock (per @handwerkerd).
  • LeakBlock is set in the Sequence, Special tab.
  • If banding occurs with the above settings or you don't care about short TEs, consider extending the excitation pulse to 8180 (per @dowdlelt)
• If using GRAPPA acceleration, use GRE with default FA=12 (good performance per @handwerkerd) or use FLEET with FA=15 and 5 dummy scans (MGH multi-echo recommendations and used by @dowdlelt), but do not use single-shot EPI.
  • Papers use FLEET with a variety of flip angles from 5, 10 and 20, so it's hard to have a specific recommendation (they all seem to work...). This may be a good reason to use GRE, which has a strong default.
  • This is set in the Sequence, Special tab.
• If processing echoes individually, consider acquiring a single-band reference image. These are useful as volume registration targets (per @dowdlelt). They can also be used in conjunction with an SBRef image with the opposite phase encoding direction for blip-up/blip-down distortion correction (also per @dowdlelt).
  • This is set in the Sequence, Special tab.

[jbteves]

This is something that has come up on numerous calls and that there is still frequent Gitter discussion about. Personally I feel strongly that there should be a deadline of having something up before OHBM starts on June 9 since it will be confusing if people see the software demo there, come to our documentation, and realize they have no idea how to acquire the data to put through tedana. It's true that we link to scientific papers but I don't believe all of the above recommendations are published anywhere. Furthermore, that's not really the focus in most papers, so it would be hard to dig out and figure out practically what to do at the console.
@emdupre @KirstieJane @tsalo @handwerkerd @dowdlelt any thoughts? Please tag anyone I missed that should be part of that discussion.

[jbteves]

Note that #282 #283 offers some practical information on acquiring multi-echo data; thanks, @handwerkerd !

[jbteves]

@emdupre per today's call I think it may be good to add the following checklist:

• link datasets and their sequence parameters (would be fixed by Update multi-echo.rst #284)
• add parameter adjustment locations for various scanner manufacturers
• link to CMRR for guidance on getting sequences at institutions

[jbteves]

@emdupre I think it's only fair that if the plan is to ask new contributors to make task-lists out of their comments, I should request the same of you 😄
If you don't want to do that, may I edit your top comment?

[emdupre]

Thanks for pinging again !! Sorry for dropping the ball. Updating the top comment now 🚀