(code: 55 - JSON_SCHEMA_VALIDATION_ERROR)

[jasongong11]

Hi, I met with this error: 1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR) ./sub-005/func/sub-005_task-game_run-01_bold.json Evidence: .CogAtlasID should match format "uri"

But there is no .CogAtlasID in my json file.

here is the json file: { "AcquisitionMatrixPE": 120, "AcquisitionNumber": 1, "AcquisitionTime": "11:35:46.767500", "BandwidthPerPixelPhaseEncode": 14.368, "BaseResolution": 120, "BodyPartExamined": "BRAIN", "ConsistencyInfo": "N4_VE11C_LATEST_20160120", "ConversionSoftware": "dcm2niix", "ConversionSoftwareVersion": "v1.0.20190410 GCC6.3.0", "DerivedVendorReportedEchoSpacing": 0.000579993, "DeviceSerialNumber": "167002", "DwellTime": 2e-06, "EchoTime": 0.028, "EchoTrainLength": 90, "EffectiveEchoSpacing": 0.000579993, "FlipAngle": 60, "ImageComments": "Unaliased_MB3_PE3", "ImageOrientationPatientDICOM": [0.997154, 0.0744459, 0.0119389, -0.0732264, 0.993949, -0.0818724], "ImageType": [ "ORIGINAL", "PRIMARY", "M", "MB", "ND", "NORM", "MOSAIC" ], "ImagingFrequency": 123.248, "InPlanePhaseEncodingDirectionDICOM": "COL", "InstitutionAddress": "Neil_Ave_1835_Columbus_Ohio_US_43210", "InstitutionName": "CCBBI", "InstitutionalDepartmentName": "Psychology", "MRAcquisitionType": "2D", "MagneticFieldStrength": 3, "Manufacturer": "Siemens", "ManufacturersModelName": "Prisma_fit", "Modality": "MR", "MultibandAccelerationFactor": 3, "PartialFourier": 0.75, "PatientPosition": "HFS", "PercentPhaseFOV": 100, "PhaseEncodingDirection": "j-", "PhaseEncodingSteps": 90, "PhaseResolution": 1, "PixelBandwidth": 2085, "ProcedureStepDescription": "SequenceRegion_Huskey", "ProtocolName": "run1", "PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_bold", "ReceiveCoilActiveElements": "HEA;HEP", "ReceiveCoilName": "Head_32", "ReconMatrixPE": 120, "RepetitionTime": 2, "SAR": 0.0307647, "ScanOptions": "PFP_FS", "ScanningSequence": "EP", "SequenceName": "epfid2d1_120", "SequenceVariant": "SK_SS", "SeriesDescription": "run1", "SeriesNumber": 16, "ShimSetting": [-59, -6182, 2274, 402, 18, -83, 92, -1], "SliceThickness": 2, "SliceTiming": [0, 0.9075, 1.815, 0.7425, 1.65, 0.5775, 1.485, 0.4125, 1.32, 0.2475, 1.155, 0.0825, 0.99, 1.8975, 0.825, 1.7325, 0.66, 1.5675, 0.495, 1.4025, 0.33, 1.2375, 0.165, 1.0725, 0, 0.9075, 1.815, 0.7425, 1.65, 0.5775, 1.485, 0.4125, 1.32, 0.2475, 1.155, 0.0825, 0.99, 1.8975, 0.825, 1.7325, 0.66, 1.5675, 0.495, 1.4025, 0.33, 1.2375, 0.165, 1.0725, 0, 0.9075, 1.815, 0.7425, 1.65, 0.5775, 1.485, 0.4125, 1.32, 0.2475, 1.155, 0.0825, 0.99, 1.8975, 0.825, 1.7325, 0.66, 1.5675, 0.495, 1.4025, 0.33, 1.2375, 0.165, 1.0725], "SoftwareVersions": "syngo_MR_E11", "SpacingBetweenSlices": 2, "StationName": "AWP167002", "TaskName": "game", "TotalReadoutTime": 0.0690191, "TxRefAmp": 262.349, "WipMemBlock": "3157f47b-3fd7-4ada-bee0-1e0421bedd0f||Sequence: R016 ve11c/master r/8780670; Nov 27 2017 15:05:12 by eja", "dcmmeta_affine": [ [-1.9943071603775024, -0.14645281434059143, 0.035923443734645844, 128.36358642578125], [-0.14889180660247803, 1.9878982305526733, -0.16153018176555634, -79.3553466796875], [0.02387780137360096, 0.1637447625398636, 1.9931426048278809, -71.53194427490234], [0.0, 0.0, 0.0, 1.0] ], "dcmmeta_reorient_transform": [ [0.0, -1.0, 0.0, 119.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0] ], "dcmmeta_shape": [120, 120, 72, 185], "dcmmeta_slice_dim": 2, "dcmmeta_version": 0.6, "global": { "const": { "AcquisitionMatrix": [120, 0, 0, 120], "AngioFlag": "N", "BitsAllocated": 16, "BitsStored": 16, "BodyPartExamined": "BRAIN", "Columns": 1080, "EchoNumbers": 1, "EchoTime": 28.0, "EchoTrainLength": 90, "FlipAngle": 60.0, "HighBit": 15, "ImageOrientationPatient": [0.99715358376331, 0.07444590681609, 0.01193890054905, -0.0732264084344, 0.99394909643602, -0.0818723811906], "ImagePositionPatient": [-997.90578678932, -1182.8637424893, 15.089827488919], "ImageType": [ "ORIGINAL", "PRIMARY", "M", "MB", "ND", "NORM", "MOSAIC" ], "ImagedNucleus": "1H", "ImagingFrequency": 123.248202, "InPlanePhaseEncodingDirection": "COL", "MRAcquisitionType": "2D", "MagneticFieldStrength": 3.0, "Manufacturer": "SIEMENS", "ManufacturerModelName": "Prisma_fit", "Modality": "MR", "NumberOfAverages": 1.0, "NumberOfPhaseEncodingSteps": 90, "PercentPhaseFieldOfView": 100.0, "PercentSampling": 100.0, "PerformedProcedureStepStartTime": "110525.499000", "PhotometricInterpretation": "MONOCHROME2", "PixelBandwidth": 2085.0, "PixelRepresentation": 0, "PixelSpacing": [2.0, 2.0], "ProtocolName": "run1", "RepetitionTime": 2000.0, "Rows": 1080, "SAR": 0.03076473040219, "SamplesPerPixel": 1, "ScanOptions": [ "PFP", "FS" ], "ScanningSequence": "EP", "SequenceName": "epfid2d1_120", "SequenceVariant": [ "SK", "SS" ], "SeriesDescription": "run1", "SeriesNumber": 16, "SeriesTime": "113551.322000", "SliceLocation": -62.571906590481, "SliceThickness": 2.0, "SmallestImagePixelValue": 0, "SoftwareVersions": "syngo MR E11", "SpacingBetweenSlices": 1.9999999532945, "StudyID": "1", "StudyTime": "110525.400000", "TransmitCoilName": "Body", "VariableFlipAngleFlag": "N", "WindowCenterWidthExplanation": "Algo1", "dBdt": 0.0}, "slices": {} }, "time": { "samples": { "AcquisitionNumber": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 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Bids_validator version 1.5.7

Many thanks!

Best, Jason

[sappelhoff]

thanks for the report @jasongong11 ... I tried to replicate this issue by bumping the bids-validator version on bids-examples and doing a travis run: https://travis-ci.org/github/bids-standard/bids-examples/builds/741338158

however, I don't see any errors of malformatted "CogAtlasID" in the absence of that field.

maybe @rwblair knows what's going on.

[jasongong11]

Thanks! @sappelhoff

I added the "CogAtlasID" field in the json file. Then the validator stopped reporting this error. I guess I can just get this around by adding the field in the json files. But still wondering what causes the issue.

Many thx again!

Best, Jason

[sappelhoff]

indeed we should solve that issue. Did you simply add any "dummy" data to that field? Or does it actually make sense for you to use it?

I would not advise to add "dummy" data just to pacify the validator :-) we'll try to be quick to solve this error

[jasongong11]

Thanks for the notice!

Yes, I arbitrarily choose a Cognitive Atlas concept and put the URL in the field. And many thanks for solving this! :D

For replicating the error here is the json file (I converted it to txt file since github does not support json file uploading)

sub-005_task-game_run-01_bold.json.txt

Thanks again!

Best, Jason

[jasongong11]

Hi,

I think I figured out what is wrong.

The two grand json files (task-game_bold.json and task-rest_bold.json) contain the CogAtlasID and I think the BIDS converter just put "TO DO" values in the field in the grand json files. But the json files for each BOLD images do not contain the field. So the validator recognizes that there should be CogAtlasID in the individual json files. And it throws the errors for each individual BOLD json files.

Thanks for your help!

Best, Jason

[sappelhoff]

Nice, that sounds like the inheritance principle was at work. This means the validator behaved as expected.

I am glad you found the issue and could resolve it. Good luck with your dataset preparation!

[jasongong11]

Thank you very much! :D

Best, Jason