Incorrect or incomplete fieldmapping protocol

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1

Dear all,

We have a SIEMENS Tim Trio 3T scanner. We have a fieldmapping protocol called “GRE_FIELD_MAPPING”. The series output is 32 DICOM images. When I convert these to nifti using dcm2niix, my json file output is below. The conversion generates a single file, which is named as GRE_FIELD_MAPPING_0015_gre_field_mapping_20220313094638_15_e2_ph

The images upon inspection resemble “phase”. However, I read that there should be 2 phase images and 1 magnitude image. This indicates that our field mapping protocol could be incorrect or incomplete. Can anyone please point me in the right direction and provide scan protocol settings which can be used for SPM?

{

    "Modality": "MR",

    "MagneticFieldStrength": 3,

    "ImagingFrequency": 123.238,

    "Manufacturer": "Siemens",

    "ManufacturersModelName": "TrioTim",

    "InstitutionName": "UMRAM //AC6DEA//Ankara",

    "InstitutionalDepartmentName": "Department",

    "InstitutionAddress": "Street StreetNo,City,District,TR,ZIP",

    "DeviceSerialNumber": "35397",

    "StationName": "MRC35397",

    "PatientPosition": "HFS",

    "ProcedureStepDescription": "AUSAF^TAMER",

    "SoftwareVersions": "syngo MR B17",

    "MRAcquisitionType": "2D",

    "SeriesDescription": "gre_field_mapping",

    "ProtocolName": "gre_field_mapping",

    "ScanningSequence": "GR",

    "SequenceVariant": "SP",

    "SequenceName": "*fm2d2r",

    "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"],

    "SeriesNumber": 15,

    "AcquisitionTime": "12:18:12.287500",

    "AcquisitionNumber": 1,

    "SliceThickness": 3,

    "SpacingBetweenSlices": 3.75,

    "SAR": 0.225768,

    "EchoNumber": 2,

    "EchoTime": 0.00765,

    "RepetitionTime": 0.4,

    "FlipAngle": 60,

    "EchoTime1": 0.00519,

    "EchoTime2": 0.00765,

    "PartialFourier": 1,

    "BaseResolution": 64,

    "ShimSetting": [

        -2208,

        8130,

        2011,

        621,

        81,

        -314,

        -244,

        81  ],

    "TxRefAmp": 300.819,

    "PhaseResolution": 1,

    "ReceiveCoilName": "32Ch_Head",

    "CoilString": "C:HEA;HEP",

    "PulseSequenceDetails": "%SiemensSeq%\\gre_field_mapping",

    "CoilCombinationMethod": "Adaptive Combine",

    "MatrixCoilMode": "SENSE",

    "PercentPhaseFOV": 100,

    "PercentSampling": 100,

    "PhaseEncodingSteps": 64,

    "AcquisitionMatrixPE": 64,

    "ReconMatrixPE": 64,

    "PixelBandwidth": 260,

    "DwellTime": 3e-05,

    "PhaseEncodingDirection": "j-",

    "SliceTiming": [

        0.20313,

        0,

        0.21094,

        0.00781,

        0.22656,

        0.02344,

        0.24219,

        0.03906,

        0.25,

        0.04688,

        0.26563,

        0.0625,

        0.27344,

        0.07031,

        0.28906,

        0.08594,

        0.30469,

        0.10156,

        0.3125,

        0.10938,

        0.32813,

        0.125,

        0.33594,

        0.13281,

        0.35156,

        0.14844,

        0.36719,

        0.16406,

        0.375,

        0.17188,

        0.39063,

        0.1875  ],

    "ImageOrientationPatientDICOM": [

        1,

        0,

        0,

        0,

        0.995227,

        -0.0975829  ],

    "ImageOrientationText": "Tra>Cor(-5.6)",

    "InPlanePhaseEncodingDirectionDICOM": "COL",

    "ConversionSoftware": "dcm2niix",

    "ConversionSoftwareVersion": "v1.0.20211006"

}
2

It sounds like the default settings of the sequence are not saving all of the files you need. This should be a quick fix, but unfortunately I don’t have a reference image for the change on the console but I believe it is in the Contrast → Dynamic Tab. A previously successful fieldmap sequence pdf suggest that the correct setting is to select “Magn./Phase” for the Reconstruction option there.

image
image1078×348 14.5 KB

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3

Thank you for your answer. By console, I understand that it is the computer which operates the scanner, am I right?

4

Sorry, yes. That is what I meant. You can make this change when you are collecting the data or (preferably) editing the sequence so that it is always saving these outputs.

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5

Thanks. I will check the console and take a look at my sequence.

6

Thanks. This was indeed the solution.

What is the best practice for fieldmap acquisitions? Shall I take one after each bold run?

7

I am not sure how something like fmriprep would use that information - most software, such as FSL, SPM and AFNI (with reverse phase encode images rather than fieldmaps) make sure of just one fieldmap to correct all of the data acquired during an acquisition. It is possible to put together your own processing pipeline that would make use of multiple fieldmaps, but I don’t think it would be that useful. I could only imagine doing something like that for very long scanning sessions (>1hr) at 7T, for example.

I tend to put a fieldmap in the middle of the scanning session, to give the participant a break, and to ‘split the difference’ of field changes and head position.

1 Like
8

Thanks for your answer. Indeed, the middle makes more sense.

1 Like