Bids validator is not articulating error

Software Support
1

Summary of what happened:

BIDS validator is triggering an error about phase encoding, but our .json file looks normal and similar to other files that have passed BIDS validation before. Not sure if we are missing something.

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

Version:

Environment (Docker, Singularity, custom installation):

Data formatted according to a validatable standard? Please provide the output of the validator:

Relevant log outputs (up to 20 lines):

Here is the error message in the slurm output:

ValueError: Fieldmap-less (SyN) estimation was requested, but PhaseEncodingDirection information appears to be absent.
INFO:    Cleanup error: while unmounting /var/apptainer/mnt/session/underlay/usr directory: device or resource busy, while unmounting /var/apptainer/mnt/session/final directory: device or resource busy

Screenshots / relevant information:

Here is the .json file:

    "Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 127.765,
	"Manufacturer": "GE",
	"ManufacturersModelName": "DISCOVERY MR750",
	"InstitutionName": "Stanford Lucas Center",
	"DeviceSerialNumber": "0000415723SCHMR2",
	"StationName": "lc3t3",
	"BodyPartExamined": "HEAD",
	"PatientPosition": "HFS",
	"ProcedureStepDescription": "Brain",
	"SoftwareVersions": "27\\LX\\MR Software release:DV26.0_R01_1725.a",
	"MRAcquisitionType": "2D",
	"SeriesDescription": "go-nogo1_spiral",
	"ProtocolName": "Bohon_EE_10282021",
	"ScanningSequence": "RM",
	"SequenceVariant": "NONE",
	"ScanOptions": "NONE",
	"ImageType": ["ORIGINAL", "PRIMARY", "OTHER"],
	"SeriesNumber": 4,
	"AcquisitionTime": "16:19:45.000000",
	"AcquisitionNumber": 1,
	"SliceThickness": 3.5,
	"SpacingBetweenSlices": 3.5,
	"EchoNumber": 1,
	"EchoTime": 0.03,
	"RepetitionTime": 2,
	"FlipAngle": 80,
	"CoilString": "8HRBRAIN",
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"AcquisitionMatrixPE": 128,
	"ReconMatrixPE": 64,
	"ParallelReductionFactorInPlane": 2,
	"PixelBandwidth": 500,
	"PhaseEncodingAxis": "i",
	"ImageOrientationPatientDICOM": [
		0.99993,
		0.00043,
		0.01148,
		0.00089,
		0.99344,
		-0.11438	],
	"InPlanePhaseEncodingDirectionDICOM": "ROW",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20210317"
2

Hi @MStern and welcome to neurostars!

I have retagged your post as software support and added in the corresponding question template. As you can see, there is some information missing that would help us address your issue. Please fill in this information (you can edit your post) so we can help.

Also, you do not have a PhaseEncodingDirection field in your JSON (it appears to be called PhaseEncodingAxis instead, which fMRIPrep will not check).

Best,
Steven

3

Closing and unlisting as duplicate of Bids validator is not articulating error p2.

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