Problems with build BIDS with fieldmap type

npdrbong · June 2, 2022, 9:29am

Hello, experts.

I have a question for how to naming dataset below into BIDS format

In the dataset, there were 6 files for b0map for bold.

I thought this data only contains phase 1/2 files and each file had a real part and imaginery part, respectively. so I configured file as below

sub-CU0009_ses-1_acq-bold_phase1.json

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 1,
    "EchoTime": 0.0065,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

sub-CU0009_ses-1_acq-bold_phase2.json

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 2,
    "EchoTime": 0.0085,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

sub-CU0009_ses-1_acq-boldImaginary_phase1

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER",
        "IMAGINARY"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 1,
    "EchoTime": 0.0065,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

sub-CU0009_ses-1_acq-boldImaginary_phase2.json

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER",
        "IMAGINARY"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 2,
    "EchoTime": 0.0085,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

sub-CU0009_ses-1_acq-boldReal_phase1

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER",
        "REAL"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 1,
    "EchoTime": 0.0065,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

sub-CU0009_ses-1_acq-boldReal_phase2.json

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 127.883,
    "Manufacturer": "GE",
    "ManufacturersModelName": "SIGNA HDx",
    "InstitutionName": "NYS PSYCHIATRIC INST",
    "DeviceSerialNumber": "0000000000001234",
    "StationName": "GEMSOW",
    "PatientPosition": "HFS",
    "SoftwareVersions": "14\\LX\\MR Software release:14.0_M5_0737.f",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "B0 Map for BOLD 39 sl",
    "ProtocolName": "B0 Map for BOLD 39 sl",
    "ScanningSequence": "RM",
    "SequenceVariant": "NONE",
    "ScanOptions": "SAT_GEMS\\FS",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "OTHER",
        "REAL"
    ],
    "SeriesNumber": 4,
    "AcquisitionTime": "18:30:25.000000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3.1,
    "SpacingBetweenSlices": 3.1,
    "EchoNumber": 2,
    "EchoTime": 0.0085,
    "RepetitionTime": 0.6,
    "FlipAngle": 45,
    "CoilString": "8HRBRAIN",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "AcquisitionMatrixPE": 64,
    "ReconMatrixPE": 64,
    "PixelBandwidth": 500,
    "PhaseEncodingAxis": "j",
    "ImageOrientationPatientDICOM": [
        0.999763,
        -0.0217294,
        -0.000885035,
        0.0217595,
        0.99953,
        0.0216068
    ],
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006",
    "Dcm2bidsVersion": "2.1.6",
    "IntendedFor": [
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-01_bold.nii.gz",
        "ses-1/func/sub-CU0009_ses-1_task-rest_run-02_bold.nii.gz"
    ]
}

and when I used this files into fmriprep, this error message came out:

ValueError: A fieldmap or phase-difference estimation type was found, but an anatomical reference (magnitude1 file) is missing.

Can you tell me what’s wrong with file naming or data?

thank you

neurolabusc · June 2, 2022, 12:05pm

The ImageType notes that your scanner was set to export complex data (IMAGINARY and REAL). These image types are not supported by BIDS. You will want to convert the complex images to magnitude and phase images supported by FSL Fugue. Here is my Matlab script. Alternatively, you could use fslcomplex.

You may want to look at my fieldmap page. I show images of the different image types (to help visual identification). I also note that different sessions from the ADNI GE scanners show different export. I provide notes on how to select the Siemens image type. However, I do not have access to GE equipment. Perhaps @mr-jaemin can provide insight.

npdrbong · June 2, 2022, 12:51pm

Thanks a lot! I will try on fslcomplex for change data into magnitude file.
have a nice day!

mr-jaemin · June 2, 2022, 2:02pm

@npdrbong it looks like B0 map was acquired using a custom PSD. Could you please upload some dataset, using this link Box?

npdrbong · June 2, 2022, 2:23pm

@mr-jaemin Thanks you! can you check the box?