Having trouble getting fMRIprep to see phasdif and magnitude images

Software Support
,
17

Thanks - I also saw this thread…

So, I have a field map which dcm2bids labeled a phasedif and two (names have changed slightly from what I mentioned above) magnitude images. Here is what I have named them.
sub-ut0010_ses-01_acq-rest_magnitude1.nii.gz
sub-ut0010_ses-01_acq-rest_magnitude2.nii.gz
sub-ut0010_ses-01_acq-rest_phasediff.nii.gz

func images are labeled
sub-ut0010_ses-01_task-rest_dir-AP_run-01_bold.nii.gz

In the JSON files, I have tried… (tried #1 below with BOTH fmriprep v 23.1.3 and 23.2.0). I should say that this DOESN’T THROW A BIDS VALIDATION ERROR when trying that.

  1. Only a B0FieldIdentifier (all above fieldmaps JSONS) and B0FieldSource (BOLD) that look like this…

FMAPS (Phasdif and Mag)

"B0FieldIdentifier": "acq_rest"

FUNC

 "B0FieldSource": "acq_rest"
  1. Only using the “IntendedForFields” in BOTH the BOLD and FIELDMAP (phasdif+magnitude) JSON

FMAP (phasdiff+magnitude)

 "IntendedFor": "ses-01/func/sub-ut0010_ses-01_task-rest_dir-AP_run-01_bold.nii.gz"

BOLD

"IntendedFor": "ses-01/fmap/sub-ut0010_ses-01_acq-rest_phasediff.nii.gz"

or

"IntendedFor": [
        "ses-01/fmap/sub-ut0010_ses-01_acq-rest_phasediff.nii.gz",
        "ses-01/fmap/sub-ut0010_ses-01_acq-rest_magnitude1.nii.gz",
        "ses-01/fmap/sub-ut0010_ses-01_acq-rest_magnitude2.nii.gz"
    ],

Still No luck; what am I missing here? Is having these magnitude images possibly causing the issues?

Also, for complete disclosure… Here is an example of my func json, obviously the IntendedFor/ B0 field changes as mentioned above.

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.223407,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "MAGNETOM Vida",
    "InstitutionName": "UT Health Austin 3T",
    "InstitutionalDepartmentName": "Radiology",
    "InstitutionAddress": "Trinity 1601B",
    "DeviceSerialNumber": "175689",
    "StationName": "AWP175689",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "SoftwareVersions": "syngo MR XA31",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "rs1-fMRI-SMS - MagnusMed",
    "ProtocolName": "rs1-fMRI-SMS - MagnusMed",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "PFP\\FS",
    "PulseSequenceName": "*epfid2d1_128",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "FMRI",
        "NONE"
    ],
    "ImageTypeText": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND"
    ],
    "NonlinearGradientCorrection": false,
    "SeriesNumber": 10,
    "AcquisitionTime": "15:13:14.395000",
    "AcquisitionNumber": 1,
    "SliceThickness": 2,
    "SpacingBetweenSlices": 2,
    "EchoTime": 0.031,
    "RepetitionTime": 1.3,
    "MTState": false,
    "FlipAngle": 77,
    "PartialFourier": 0.75,
    "BaseResolution": 128,
    "ShimSetting": [
        -1765,
        -1885,
        9387,
        282,
        -277,
        -33,
        235,
        108
    ],
    "TxRefAmp": 322.4,
    "PhaseResolution": 1,
    "ReceiveCoilName": "HeadNeck_64_CS",
    "ReceiveCoilActiveElements": "HC1-7",
    "CoilString": "HeadNeck_64_CS",
    "PulseSequenceDetails": "%SiemensSeq%\\ep2d_bold",
    "RefLinesPE": 22,
    "CoilCombinationMethod": "Sum of Squares",
    "MultibandAccelerationFactor": 6,
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 96,
    "PartialFourierDirection": "PHASE",
    "PhaseEncodingSteps": 128,
    "FrequencyEncodingSteps": 128,
    "AcquisitionMatrixPE": 128,
    "ReconMatrixPE": 128,
    "BandwidthPerPixelPhaseEncode": 10.557,
    "ParallelAcquisitionTechnique": "SMS",
    "EffectiveEchoSpacing": 0.00074003,
    "DerivedVendorReportedEchoSpacing": 0.00074003,
    "AcquisitionDuration": 402.18,
    "TotalReadoutTime": 0.0939838,
    "PixelBandwidth": 1628,
    "DwellTime": 2.4e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59,
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59,
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59,
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59,
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59,
        0,
        0.69,
        0.1,
        0.7875,
        0.1975,
        0.8875,
        0.295,
        0.985,
        0.395,
        1.0825,
        0.4925,
        1.1825,
        0.59
    ],
    "ImageOrientationPatientDICOM": [
        0.998889,
        0.0368238,
        0.0294159,
        -0.0392464,
        0.995475,
        0.0865407
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20230411",
    "Dcm2bidsVersion": "3.1.0",
    "B0FieldSource": "acq_rest"
}