Check if current standard accomodated MPM/hMRI required metadata

[KirstieJane]

Action for @christophephillips to map the metadata that is required for the hmri toolbox into the BEP001 recommendations and to check whether we're all covered.

[ChristophePhillips]

Here are what I found in term of metadata for the MPM sequence

Specific acquisition parameters

This list the parameters as being used by the hMRI toolbox, as of September 2019.

---

Fieldnames queried by the hMRI toolbox	Fieldnames for BIDS	Already existing in BIDS?	Description/comments
GENERAL
RepetitionTime	RepetitionTimeExcitation	y
EchoTime	EchoTime	y
FlipAngle	FlipAngle	y
NAMING
ScanningSequence	ScanningSequence	y
SequenceName	SequenceName	y
ProtocolName	ProtocolName	N	What does it correspond to exactly? Add def in BIDS?
ManufacturerModelName	ManufacturerModelName	y
RF SPOILING
RFSpoilingPhaseIncrement	SpoilingRFPhaseIncrement	y
spoilingGradientMoment	SpoilingGradientMoment	y
spoilingGradientDuration	SpoilingGradientDuration	y
B1 MAPPING
B1mapNominalFAValues	B1mapNominalFAValues	N	Extend FlipAngle with NominalFlipAngle?
B1mapMixingTime	MixingTime	N	Anything close?
epiReadoutDuration	epiReadoutTime	N	Is this equivalent to TotalReadoutTime?
PhaseEncodingDirectionSign	PhaseEncodingDirectionSign	N	Same as SliceEncodingDirection?
BandwidthPerPixelRO	BandwidthPerPixelRO	N	Seems linked to EffectiveEchoSpacing but?
PELinesPAT	PELinesPAT	N	??
NumberOfMeasurements	NumberOfMeasurements	N	??
OTHERS
RepetitionTimes	RepetitionTimesExcitation	N	See extra 's', used(?) in case multiple TRs are passed -> not standard BIDS anyway

Comments:

• NAMING. There are many other fields regarding the hardware, see the Scanner hardware section of this file and the same goes for the Sequence Specifics.
• RF SPOILING. There are 2 more fields SpoilingState (true/false) and SpoilingType (RF, GRADIENT, or COMBINED), see bottom of Sequence Specifics section.
• B1 MAPPING. These are not part of the current proposal and would have to be added. What is missing is a clear definition of each of these parameters...

[tiborauer]

• What is ProtocolName for?
• Does B1 map has 'normal' FlipAngle apart from NominalFlipAngle? How do you get NominalFlipAngle?
• How do you get B1mapMixingTime?
• How do you get epiReadoutDuration? TotalReadoutTime "is NOT the actual, physical duration of the readout train", if that is what you after.
• Is PhaseEncodingDirectionSign the same as PhaseEncodingDirectionPositive (in Siemens)? I am not sure whether it is available in DICOMs from other vendors.
• How do you get BandwidthPerPixelRO? I know about BandwidthPerPixelPhaseEncode, but it is along the other axis.
• What is PELinesPAT?
• What is NumberOfMeasurements?

[KirstieJane]

Some notes from the conversation on 9 October.

• Can we match up each of these metadata fields to the dicom tags that they allign to?
  • We have an action going forwards to harmonise the current terms with the additional metadata terms. Plan is to clearly define the needed information first.
• Are there some metadata fields listed above that are actually collections of other metadata from the scanner? We decided that it makes most sense to define the fields that come off the scanner rather than calculated ones.
  • Search for the "Method-specific priority levels for qMRI metadata" and "qMRI applications that can be derived from an existing grouping suffix" sections in the https://github.com/bids-standard/bep001/blob/indexable_metadata/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md file
• It would be great to be clear about which of the metadata fields are required vs desirable.

[ChristophePhillips]

I have updated the list of parameters, see here, for the MPM sequence.

Good news: most of them fit with the current BEP001, only a handful should/could be added. And since BIDS relies on the 80/20 Pareto's principe, this may not be needed actually.

The description of the field maps, or raw data leading to the estimation of these field maps to be more precise, remains open to discussion at the moment, cf #51, #67, #73, #80.

[agahkarakuzu]

Thank you @ChristophePhillips! I was just updating the MPM description on the suffix table and adding a link to the protocols suggested by hMRI (https://owncloud.gwdg.de/index.php/s/iv2TOQwGy4FGDDZ) :)