OpenNeuro and BIDS validator (v. 1.14.0) detect errors code 10, 15 and 50 but files already contain repetition, echo time and task name [SOLVED]

, ,
1

Hi there,

I am trying to upload my BIDS formatted dataset on Open Neuro (first-time user) and I encounter errors that I do not understand and cannot fix. I tried running it though BIDS validator (version 1.14.0) as recommended by Open Neuro help desk but it basically gives me the same error.
I have attached a screenshot of the BIDS validator error listing I get below (it’s identical in OpenNeuro):

BIDS_errors
BIDS_errors776×442 50.3 KB

It affects my func (code 10 and 50) and fmap (code 15) json files for all subjects and runs.
The issue is that these parameters it says are missing are actually there in the json files.
I looked at previous posts with similar errors and tried using a json linter to check the syntax validity but it seems my files are valid.

Here is an example of one of my json file content (bold.json):

{
	"acqpar": [
		{
			"Modality": "MR",
			"Manufacturer": "SIEMENS ",
			"InstitutionName": "XXX ",
                        "TaskName": "Naming to definitions",
			"InstitutionAddress": "XXX",
			"ReferringPhysicianName": "SNAME ",
			"StationName": "AWP66023",
			"StudyDescription": "Brain Research_Current^SNAME",
			"ProcedureCodeSequence": [
				{
					"CodeValue": "MRBR"
				}
			],
			"SeriesDescription": "AP_MB4_BOLD_DEFN_B1 ",
			"InstitutionalDepartmentName": "XXX ",
			"PerformingPhysicianName": "  ",
			"OperatorsName": "  ",
			"ManufacturerModelName": "Prisma",
			"BodyPartExamined": "BRAIN ",
			"ScanningSequence": "EP",
			"SequenceVariant": "SK",
			"ScanOptions": "PFP\\FS",
			"MRAcquisitionType": "2D",
			"SequenceName": "*epfid2d1_72",
			"AngioFlag": "N ",
			"SliceThickness": 2.5999999046326,
			"RepetitionTime": 1000,
			"EchoTime": 30,
			"NumberOfAverages": 1,
			"ImagingFrequency": 123.241996,
			"ImagedNucleus": "1H",
			"EchoNumbers": 1,
			"MagneticFieldStrength": 3,
			"SpacingBetweenSlices": 2.6000000625534,
			"NumberOfPhaseEncodingSteps": 63,
			"EchoTrainLength": 63,
			"PercentSampling": 100,
			"PercentPhaseFieldOfView": 100,
			"PixelBandwidth": 2570,
			"DeviceSerialNumber": "66023 ",
			"SoftwareVersions": "syngo MR E11",
			"ProtocolName": "AP_MB4_BOLD_DEFN_B1 ",
			"TransmitCoilName": "Body",
			"AcquisitionMatrix": [72,0,0,72],
			"InPlanePhaseEncodingDirection": "COL ",
			"FlipAngle": 80,
			"VariableFlipAngleFlag": "N ",
			"SAR": 0.06474366161484001,
			"PatientPosition": "HFS ",
			"StudyID": "1 ",
			"SeriesNumber": 11,
			"AcquisitionNumber": 11,
			"InstanceNumber": 11,
			"ImagePositionPatient": [-639.66156442819,-692.18637022924,2.7903423194668],
			"ImageOrientationPatient": [0.99699876671064,0.03325176011183,-0.0699126571296,-0.0348159321823,0.9991672722264801,-0.0212747027657],
			"FrameOfReferenceUID": "1.3.12.2.1107.5.2.43.66023.1.20230317114445682.0.0.0",
			"SliceLocation": -57.814503894139,
			"SamplesPerPixel": 1,
			"PhotometricInterpretation": "MONOCHROME2 ",
			"Rows": 504,
			"Columns": 504,
			"PixelSpacing": [2.638888835907,2.638888835907],
			"BitsAllocated": 16,
			"BitsStored": 12,
			"HighBit": 11,
			"PixelRepresentation": 0,
			"SmallestImagePixelValue": 0,
			"LargestImagePixelValue": 1454,
			"WindowCenter": 612,
			"WindowWidth": 1261,
			"WindowCenterWidthExplanation": "Algo1 ",					
		}
	]
}

Any idea where the errors are coming from? What am I missing here?
Thank you for reading this!
Angelique

2

Hi @avolfart and welcome to neurostars!

I think you have to remove this (and the closing bracket } ). Usually the fields are not nested in the JSON file.

Best,
Steven

3

Hi Steven,

Thank you for your reply.
The json file that is automatically extracted from DICOM files is actually bigger than what I copied here but I was not allowed to post it all because of character limits and thus I only kept lines that seemed relevant for my question. You’re right it contains a lot of nesting…
Does it mean I should not upload the “native” json file I get when converting DICOM to .nii (done in SPM12) and reduce its length to only a subset of lines?
I will try removing just the “acqpar” nesting and keep you updated.

Best,
Angelique

4

Hi @avolfart,

I don’t know the specifics of converting in SPM, but I recommend using dcm2niix (and tools that invoke it such as dcm2bids and bidscoin) for better BIDS validity (and therefore openneuro compatibility as well).

Best,
Steven

5

Hi Steven,

Thanks to your comment I managed to find out what the issue was. It was related to the DICOM to NifTI conversion function used in the matlab script I was provided with and which was extracting json files in a weird format.
My dataset passes the BIDS validator now, thank you very much again for your help!

Best,
Angelique