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bids-standard / bids-examples

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.
http://bids-standard.github.io/bids-examples/
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genetics_ukbb missing EchoTime1 and EchoTime2 #401

Closed rwblair closed 1 year ago

rwblair commented 1 year ago

https://github.com/bids-standard/bids-specification/blob/master/src/schema/rules/checks/fmap.yaml

https://github.com/bids-standard/bids-examples/tree/master/genetics_ukbb/sub-02/fmap Has fmap and magnitude1 niftis but no json for them.

rwblair commented 1 year ago

Fails both schema.rules.checks.fmap.EchoTime12DifferenceUnreasonable schema.rules.sidecars.fmap.MRIFieldmapPhaseDifferencePhasediff

rwblair commented 1 year ago

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#types-of-fieldmaps

mentioned as a good example in spec. Maybe remove fmaps, this ds is for showing of genetics part off spec.

Remi-Gau commented 1 year ago

https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#types-of-fieldmaps

mentioned as a good example in spec. Maybe remove fmaps, this ds is for showing of genetics part of spec.

agreed

sappelhoff commented 1 year ago

cc @CPernet

CPernet commented 1 year ago

this is the data we got from looking at UKBB - I do not have them, so cannot possibly tell what values are - maybe the extension lead author knows? @claramoreau9

effigies commented 1 year ago

Looking through the exam card (https://www.fmrib.ox.ac.uk/ukbiobank/protocol/V4_23092014.pdf), I can't find anything that would indicate a pair of EchoTimes. There's an "SWI" acquisition with TE 1, but no second TE unless it's assumed to be 2*TE1 (or something). Someone with more familiarity with Skyra exam cards might be able to pull something out.