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MPM_parameter_list.md

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MPM sequence

Specific acquisition parameters

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

Fieldnames queried by the hMRI toolbox Fieldnames for BIDS In BIDS or
description/comments		 Scaling
MACHINE NAMING
Manufacturer Manufacturer YES /
ManufacturerModelName ManufacturersModelName YES /
DeviceSerialNumber DeviceSerialNumber YES /
StationName StationName YES /
MagneticFieldStrength MagneticFieldStrength YES
SEQUENCE NAMING /
ScanningSequence ScanningSequence YES /
SequenceName SequenceName YES /
ProtocolName PulseSequenceDetails YES, assuming it fits /
Main acquisition parameters
RepetitionTime RepetitionTimeExcitation YES ms​ ➡️ ​s
EchoTime EchoTime YES ms ➡️ s
FlipAngle FlipAngle YES /
MT MTState YES /
IN-PLANE ENCODING
NumberOfMeasurements NumberShots YES, assuming it fits /
epiReadoutDuration TotalReadoutTime YES, assuming it fits ms ➡️ s
PhaseEncodingDirectionSign PhaseEncodingDirectionSign NO, it should be SliceEncodingDirection but here only the sign is known.
RF CORRECTION in al_B1mapping and mtflash3d sequences
RFSpoilingPhaseIncrement SpoilingRFPhaseIncrement YES
spoilingGradientMoment SpoilingGradientMoment YES
spoilingGradientDuration SpoilingGradientDuration YES ms ➡️ s
3D_EPI FOR B1 MAPPING
B1mapNominalFAValues NominalFAValues NO
B1mapMixingTime MixingTime NO ms ➡️ s

Comments:

Most metadata already exist in BIDS-BEP001.

A few things are assumed to match and others should/could be added:

  • ProtocolName sounds like PulseSequenceDetails, at least they can store a sequence identification code

  • NumberOfMeasurements, used to get the B1mapNominalFAValues, could be the same as NumberShots, defined as

The number of RF excitations need to reconstruct a slice or volume. Please mind that this is not the same as Echo Train Length which denotes the number of lines of k-space collected after an excitation.

To be checked.

  • epiReadoutDuration sounds quite like TotalReadoutTime, defined as

    This is actually the "effective" total readout time , defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train.

    What about the potential acceleration factors?

  • PhaseEncodingDirectionSign is only about the sign of the phase encoding direction but NOT the direction itself. Or should direction and sign be extracted ? Both direction and sign are coded by SliceEncodingDirection with values i, j, k, i-, j-, k-. To be further investigated to to reliably extract this from the DICOM header.

  • B1 mapping (B1+) parameters are not (yet) part of BEP001 and would have to be added. What is missing is a clear definition of each of these parameters...

B1+ parameters

Some information from Evelyne Balteau and a figure.

  • MixingTime is something typical for a stimulated echo sequence (pulse 1 - dephasing - pulse 2 - mixing time: magnetisation is stored along longitudinal axis, no further dephasing - pulse 3 - rephasing and recording of stimulated echo aka STE). This type of sequence is mainly used in MR spectroscopy... So it is "just" a matter of adding a standard parameter, when applicable, called "MixingTime"... Here we also acquire a standard spin-echo (aka SE) image during the mixing time (because not all the spins are following the STE pathway determined with a purely 90-90-90 pulse sequence).

  • FlipAngle and NominalFAValues. The standard FA here is the alpha_exc (it is likely to be 90°), while the "B1 map nominal FA values" are the series of values used for alpha. E.g. in our B1 mapping case, we have 11 pairs of SE/STE volumes.

Illustration of the B1+ mapping sequence: