-
Notifications
You must be signed in to change notification settings - Fork 1
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Deprecate phase and magnitude suffixes in favor of part and echo entities for field maps #3
Comments
To clarify with examples:
|
Does anyone have any idea how we would want to support phase-difference images here? Would a new suffix like |
Phase[diff] are typically not acquired with EPI (which would imply analytically invert a generally nondiffeomorphic deformation). _fieldmap are not acquired with EPI. Why epi - which is the only sequence-mapped suffix allowed under fmap/ that doesn't actually measure the field map? |
The reason is that I don't know that much about the sequences going into field maps 😞. I just assumed phase-difference field maps were EPIs with short echo times. It sounds like the two ideas you proposed in bids-standard/bids-specification#424 would be much more accurate, so I'll post them here. From bids-standard/bids-specification#424 (comment):
From bids-standard/bids-specification#424 (comment):
One thing I would note about the Regarding the |
Gotcha :). This is why we are working through PR, so I'm happy to see that there's not a strong opinion behind that proposal and therefore, you are looking forward to make all the changes it takes. Thanks for pushing on this -a bit abandoned- part of the MRI specifications.
Yes, I don't love these particular two. To make it worse - for instance, Philips generates fieldmaps in Hz (meaning, they are phase-unwrapped, ready to use), and I have no clue as to whether they use GRE and use software to provide you the b0_map (that's apparently their vendored sequence name) or they use SEI. Also, it is not unthinkable at all that, e.g. Siemens, starts spitting phase difference maps with the phase unwrapped. So, the definite, more compact way to represent these fieldmaps would be:
And make MANDATORY two metadata fields: {
"Units": "rad/s",
"PhasedWrapped": true
} When units are not When units are Finally, when units are |
And, if you don't want to reuse
with the big B (do not please suggest a small b). And if you want to be a purist:
or even more so:
More context for this is given here: https://www.nipreps.org/sdcflows/api/sdcflows.workflows.fit.fieldmap.html |
I like both
Two things I want to take into account from the qMRI BEP:
|
FWIW, |
Yes absolutely. If others agree, then I think we could propose these new suffixes in BIDS 1.x and then drop the old versions in 2.0. |
Sounds good! |
If bids-standard/bids-specification#424 is merged, then there will be an entity that delineates magnitude/phase in the specification. There already is one that delineates multi-echo data (echo). These two entities can replace the existing func suffix “phase” and the existing fmap suffixes “phase1”, “phase2”, “magnitude1”, and “magnitude2”. I’m not sure how best to label “phasediff” with the current proposal, but I’m sure we can figure out a way.
Original title: Deprecate phase, phase1, phase2, phasediff, magnitude1, magnitude2 suffixes in favor of part and echo entities
Original authors: @tsalo
The text was updated successfully, but these errors were encountered: