BIDS validator 1.9.3 (containerised) raises errors code 10 and 50 and warning code 13 for file containing repetition time, task name, and slice timing

1

Hi there!
I’m trying to run fMRIprep on a dataset collected locally, but before I do that I’m parsing the dataset with a containerised version of the bids validator (v1.9.3).
The validator raises two error codes and a warning code (specifically, REPETITION_TIME_MUST_DEFINE, TASK_NAME_MUST_DEFINE, and SLICE_TIMING_NOT_DEFINED) on a set of files that do have all those labels.
I’m reporting the json file here, what am I missing?

json file [expand] 

{
    "Modality": "MR", 
    "MagneticFieldStrength": 3, 
    "ImagingFrequency": 123.256, 
    "Manufacturer": "Siemens", 
    "ManufacturersModelName": "Prisma", 
    "BodyPartExamined": "BRAIN", 
    "PatientPosition": "HFS", 
    "ProcedureStepDescription": "MR_du_Cerveau_Recherche", 
    "SoftwareVersions": "syngo_MR_E11", 
    "MRAcquisitionType": "2D", 
    "SeriesDescription": "Rest_1", 
    "ProtocolName": "Rest_1", 
    "ScanningSequence": "EP", 
    "SequenceVariant": "SK", 
    "ScanOptions": "PFP_FS", 
    "SequenceName": "_epfid2d1_112", 
    "ImageType": [
        "ORIGINAL", 
        "PRIMARY", 
        "M", 
        "ND", 
        "MOSAIC"
    ], 
    "SeriesNumber": 6, 
    "AcquisitionTime": "15:40:12.735000", 
    "AcquisitionNumber": 1, 
    "SliceThickness": 2, 
    "SpacingBetweenSlices": 2, 
    "SAR": 0.0492724, 
    "EchoTime": 0.032, 
    "RepetitionTime": 1.25, 
    "FlipAngle": 58, 
    "PartialFourier": 0.875, 
    "BaseResolution": 112, 
    "ShimSetting": [
        683, 
        -11625, 
        6659, 
        189, 
        5, 
        -119, 
        -78, 
        30
    ], 
    "TxRefAmp": 245.455, 
    "PhaseResolution": 1, 
    "ReceiveCoilName": "HeadNeck_64", 
    "ReceiveCoilActiveElements": "HC1-7;NC1", 
    "PulseSequenceDetails": "%SiemensSeq%_ep2d_bold", 
    "RefLinesPE": 12, 
    "CoilCombinationMethod": "Sum_of_Squares", 
    "ConsistencyInfo": "N4_VE11C_LATEST_20160120", 
    "MultibandAccelerationFactor": 5, 
    "PercentPhaseFOV": 100, 
    "PercentSampling": 100, 
    "EchoTrainLength": 98, 
    "PhaseEncodingSteps": 98, 
    "AcquisitionMatrixPE": 112, 
    "ReconMatrixPE": 112, 
    "BandwidthPerPixelPhaseEncode": 15.664, 
    "EffectiveEchoSpacing": 0.000570006, 
    "DerivedVendorReportedEchoSpacing": 0.000570006, 
    "TotalReadoutTime": 0.0632706, 
    "PixelBandwidth": 2230, 
    "DwellTime": 2e-06, 
    "PhaseEncodingDirection": "j-", 
    "SliceTiming": [
        0, 
        0.6575, 
        0.0825, 
        0.74, 
        0.165, 
        0.82, 
        0.2475, 
        0.9025, 
        0.33, 
        0.985, 
        0.41, 
        1.0675, 
        0.4925, 
        1.1475, 
        0.575, 
        0, 
        0.6575, 
        0.0825, 
        0.74, 
        0.165, 
        0.82, 
        0.2475, 
        0.9025, 
        0.33, 
        0.985, 
        0.41, 
        1.0675, 
        0.4925, 
        1.1475, 
        0.575, 
        0, 
        0.6575, 
        0.0825, 
        0.74, 
        0.165, 
        0.82, 
        0.2475, 
        0.9025, 
        0.33, 
        0.985, 
        0.41, 
        1.0675, 
        0.4925, 
        1.1475, 
        0.575, 
        0, 
        0.6575, 
        0.0825, 
        0.74, 
        0.165, 
        0.82, 
        0.2475, 
        0.9025, 
        0.33, 
        0.985, 
        0.41, 
        1.0675, 
        0.4925, 
        1.1475, 
        0.575, 
        0, 
        0.6575, 
        0.0825, 
        0.74, 
        0.165, 
        0.82, 
        0.2475, 
        0.9025, 
        0.33, 
        0.985, 
        0.41, 
        1.0675, 
        0.4925, 
        1.1475, 
        0.575
    ], 
    "ImageOrientationPatientDICOM": [
        0.999961, 
        -0.00233497, 
        -0.0085507, 
        -4.80371e-08, 
        0.964678, 
        -0.263434
    ], 
    "ImageOrientationText": "Tra>Cor(-15.3)>Sag(-0.5)", 
    "InPlanePhaseEncodingDirectionDICOM": "COL", 
    "ConversionSoftware": "dcm2niix", 
    "ConversionSoftwareVersion": "v1.0.20211006", 
    "Dcm2bidsVersion": "2.1.4", 
    "TaskName": "Rest"
}

Thank you!
Stefano

2

Hello! Have you solved this problem? I met a similar problem today and don’t know what to do…
(really looking forward to your reply! Many thanks!

3

Hey there!

I did solve the issue, but it was a very absurd chain of errors. In my case, it was an invalid character somewhere else in the json that cascaded into this errors. Worth checking the jsons with a json linter, to see if invalid characters are present!

4

Hi! It seems my json files and your json file are all valid because they are generated by the same code. But I solved the problem by upgrading the fMRIprep to the latest version. Many thanks again!