Fmriprep 23.2.0 didn't do sesceptibility distortion correction

Software Support
1

Summary of what happened:

the fmriprep output .HTML report showed it didn’t run SDC.

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker --fs-license-file /host/license.txt /host/bids /host/fmriprep  -w host/fmriprep_workDir  --ignore slicetiming --skip_bids_validation --me-output-echos

Version:

23.2.0

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

BIDS Validation report

Put BIDS validation report here

Screenshots / relevant information:

Here is my input files list:

image
image964×619 235 KB

And here is the report from fmriprep:
image
image1029×457 61.7 KB

Where the ‘susceptibility distortion correction: None’

Thank you so much for any help!

2

Hi @Hongxiu_Jiang,

How are you setting up SDC? IntendedFor or B0FieldIdentifier/Source method? It would help to show us the fmap jsons. Also, it looks like the session name got wrapped in to the subject name, so it would help to fix that, and then provide us the BIDS validation report.

Best,
Steven

3

Thank you for your quick reply.

I’m not familiar with IntendedFor or B0FieldIdentifier/Source. I was not asked to do anything related to them when using bidscoin.
(btw, I used “dicomsorter, bidsmapper, bidscoiner” to convert dicom to nifti in bids format)

I guess the session name would be fine, because it was taken as the subject name in my analysis.

The bids validation report showed one error, which I don’t know how to fix it:

image
image1387×613 162 KB

The fmap json files as follows:
AP:

{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.26,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Prisma_fit",
    "DeviceSerialNumber": "167017",
    "StationName": "MRC35056",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr. Chai",
    "SoftwareVersions": "syngo MR E11",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "FieldMapping-3mm_se_AP",
    "ProtocolName": "FieldMapping-3mm_se_AP",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "FS",
    "SequenceName": "epse2d1_80",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "NORM",
        "MOSAIC"
    ],
    "SeriesNumber": 9,
    "AcquisitionTime": "14:59:54.772500",
    "AcquisitionNumber": 1,
    "SliceThickness": 3,
    "SpacingBetweenSlices": 3,
    "SAR": 0.314045,
    "EchoTime": 0.0512,
    "RepetitionTime": 5.32,
    "FlipAngle": 90,
    "PartialFourier": 1,
    "BaseResolution": 80,
    "ShimSetting": [
        211,
        -11934,
        -6310,
        487,
        11,
        -60,
        4,
        20
    ],
    "TxRefAmp": 231.041,
    "PhaseResolution": 1,
    "ReceiveCoilName": "Head_32",
    "ReceiveCoilActiveElements": "HEA;HEP",
    "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
    "WipMemBlock": "8c5ee6b8-fef7-4c78-8a08-9bf145a3e8ee||Sequence: R016 ve11c/master r/34fb20f; Nov 20 2017 15:30:40 by eja",
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE11C_LATEST_20160120",
    "MatrixCoilMode": "SENSE",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 80,
    "PhaseEncodingSteps": 80,
    "AcquisitionMatrixPE": 80,
    "ReconMatrixPE": 80,
    "BandwidthPerPixelPhaseEncode": 25,
    "EffectiveEchoSpacing": 0.0005,
    "DerivedVendorReportedEchoSpacing": 0.0005,
    "TotalReadoutTime": 0.0395,
    "PixelBandwidth": 2315,
    "DwellTime": 2.7e-06,
    "PhaseEncodingDirection": "j-",
    "SliceTiming": [
        5.2125,
        5.125,
        5.035,
        4.9475,
        4.86,
        4.77,
        4.6825,
        4.595,
        4.505,
        4.4175,
        4.33,
        4.24,
        4.1525,
        4.065,
        3.975,
        3.8875,
        3.8,
        3.71,
        3.6225,
        3.535,
        3.445,
        3.3575,
        3.27,
        3.18,
        3.0925,
        3.005,
        2.915,
        2.8275,
        2.74,
        2.65,
        2.5625,
        2.475,
        2.385,
        2.2975,
        2.21,
        2.12,
        2.0325,
        1.945,
        1.855,
        1.7675,
        1.68,
        1.59,
        1.5025,
        1.415,
        1.325,
        1.2375,
        1.15,
        1.06,
        0.9725,
        0.885,
        0.795,
        0.7075,
        0.62,
        0.53,
        0.4425,
        0.355,
        0.265,
        0.1775,
        0.09,
        0
    ],
    "ImageOrientationPatientDICOM": [
        1,
        -0.000366928,
        -0.000743092,
        -1.03987e-10,
        0.896645,
        -0.44275
    ],
    "ImageOrientationText": "Tra>Cor(-26.3)>Sag(-0.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006"
}
PA:
{
    "Modality": "MR",
    "MagneticFieldStrength": 3,
    "ImagingFrequency": 123.26,
    "Manufacturer": "Siemens",
    "ManufacturersModelName": "Prisma_fit",
    "DeviceSerialNumber": "167017",
    "StationName": "MRC35056",
    "BodyPartExamined": "BRAIN",
    "PatientPosition": "HFS",
    "ProcedureStepDescription": "Functional^Dr. Chai",
    "SoftwareVersions": "syngo MR E11",
    "MRAcquisitionType": "2D",
    "SeriesDescription": "FieldMapping-3mm_se_PA",
    "ProtocolName": "FieldMapping-3mm_se_PA",
    "ScanningSequence": "EP",
    "SequenceVariant": "SK",
    "ScanOptions": "FS",
    "SequenceName": "epse2d1_80",
    "ImageType": [
        "ORIGINAL",
        "PRIMARY",
        "M",
        "ND",
        "NORM",
        "MOSAIC"
    ],
    "SeriesNumber": 10,
    "AcquisitionTime": "15:00:34.205000",
    "AcquisitionNumber": 1,
    "SliceThickness": 3,
    "SpacingBetweenSlices": 3,
    "SAR": 0.314045,
    "EchoTime": 0.0512,
    "RepetitionTime": 5.32,
    "FlipAngle": 90,
    "PartialFourier": 1,
    "BaseResolution": 80,
    "ShimSetting": [
        211,
        -11934,
        -6310,
        487,
        11,
        -60,
        4,
        20
    ],
    "TxRefAmp": 231.041,
    "PhaseResolution": 1,
    "ReceiveCoilName": "Head_32",
    "ReceiveCoilActiveElements": "HEA;HEP",
    "PulseSequenceDetails": "%CustomerSeq%\\cmrr_mbep2d_se",
    "WipMemBlock": "fc35aa4b-60a6-42db-96ef-d3530952aa11||Sequence: R016 ve11c/master r/34fb20f; Nov 20 2017 15:30:40 by eja",
    "CoilCombinationMethod": "Sum of Squares",
    "ConsistencyInfo": "N4_VE11C_LATEST_20160120",
    "MatrixCoilMode": "SENSE",
    "PercentPhaseFOV": 100,
    "PercentSampling": 100,
    "EchoTrainLength": 80,
    "PhaseEncodingSteps": 80,
    "AcquisitionMatrixPE": 80,
    "ReconMatrixPE": 80,
    "BandwidthPerPixelPhaseEncode": 25,
    "EffectiveEchoSpacing": 0.0005,
    "DerivedVendorReportedEchoSpacing": 0.0005,
    "TotalReadoutTime": 0.0395,
    "PixelBandwidth": 2315,
    "DwellTime": 2.7e-06,
    "PhaseEncodingDirection": "j",
    "SliceTiming": [
        5.2125,
        5.125,
        5.035,
        4.9475,
        4.86,
        4.77,
        4.6825,
        4.595,
        4.505,
        4.4175,
        4.33,
        4.24,
        4.1525,
        4.065,
        3.975,
        3.8875,
        3.8,
        3.71,
        3.6225,
        3.535,
        3.445,
        3.3575,
        3.27,
        3.18,
        3.0925,
        3.005,
        2.915,
        2.8275,
        2.74,
        2.65,
        2.5625,
        2.475,
        2.385,
        2.2975,
        2.21,
        2.12,
        2.0325,
        1.945,
        1.855,
        1.7675,
        1.68,
        1.59,
        1.5025,
        1.415,
        1.325,
        1.2375,
        1.15,
        1.06,
        0.9725,
        0.885,
        0.795,
        0.7075,
        0.62,
        0.53,
        0.4425,
        0.355,
        0.265,
        0.1775,
        0.09,
        0
    ],
    "ImageOrientationPatientDICOM": [
        1,
        -0.000366928,
        -0.000743092,
        -1.03987e-10,
        0.896645,
        -0.44275
    ],
    "ImageOrientationText": "Tra>Cor(-26.3)>Sag(-0.0)",
    "InPlanePhaseEncodingDirectionDICOM": "COL",
    "ConversionSoftware": "dcm2niix",
    "ConversionSoftwareVersion": "v1.0.20211006"
}

Thank you!

4

Hi @Hongxiu_Jiang,

In the future. please format computer text (like the JSON contents) as code using the </> button in the text editor. You can see I did that for you this time.

It looks like you are missing the TaskName field from your BOLD JSONS. Something like "TaskName": "Movie Cloudy" would suffice. I would also fix the session naming (change sub-C010session2 to sub-C010/ses-2/ and fix the filenames accordingly). Also, I imagine you want the task label just to be task-MovieCloudy, and instead have the acq-fmri3mmiso and dir-AP labels, since that information is not about the task.

IntendedFor is a fmap JSON field that maps to the BOLD file you want to apply it to, relative to the inside of the subject folder, for example (after applying the name changes I suggested):

"IntendedFor": ["ses-2/func/sub-C010_ses-2_task-MovieCloudy_acq-fmri3mmiso_dir-AP_run-1_echo-1_bold.nii.gz", ADD_OTHERS_HERE]

For B0FieldSource/Identifier, in the fmap json you give the fmap a name, such as

"B0FieldIdentifier": "fmap_for_cloudy_run1"

and then in any BOLD json you want to apply that to, put in

"B0FieldSource": "fmap_for_cloudy_run1"

The B0FieldSource/Identifier method takes precedence over IntendedFor if both are specified.

Best,
Steven

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