BIDS 1.9.0 for _PD suffix: (code: 1 - NOT_INCLUDED)

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1

Hello humans!

I am running BIDS validation on Healthy Brain Network (HBN) MRI data.

Site- subjects have data as:

<…>_FLAIR.json
<…>_FLAIR.nii.gz
<…>_MT-off_PD.json
<…>_MT-off_PD.nii.gz
<…>_MT-on_PD.json
<…>_MT-on_PD.nii.gz
<…>_T1w.json
<…>_T1w.nii.gz

According to BIDS website:

image
image1156×568 35.4 KB

image
image1174×1224 89.8 KB

I am confused which suffix should i use instead of _PD - PDw or PDmap?

Here’s _PD.json content example:

{
    "InPlanePhaseEncodingDirectionDICOM": "ROW", 
    "ProcedureStepDescription": "CMI_HBN", 
    "DeviceSerialNumber": "26121", 
    "AcquisitionMatrixPE": 256, 
    "ImageOrientationPatientDICOM": [
        0.0261769, 
        0.999657, 
        1.918e-08, 
        0.059286, 
        -0.00155244, 
        -0.99824
    ], 
    "ManufacturersModelName": "Avanto", 
    "ProtocolName": "MT_OFF_-SAG", 
    "RepetitionTime": 0.03, 
    "MagneticFieldStrength": 1.5, 
    "PhaseEncodingSteps": 191, 
    "MRAcquisitionType": "3D", 
    "ParallelReductionFactorInPlane": 2, 
    "SliceThickness": 1, 
    "DwellTime": 5.6e-06, 
    "TxRefAmp": 236.752, 
    "SAR": 0.0068763, 
    "ConversionSoftware": "dcm2niix", 
    "ScanningSequence": "GR", 
    "Manufacturer": "Siemens", 
    "PercentPhaseFOV": 100, 
    "ReconMatrixPE": 256, 
    "FlipAngle": 15, 
    "SeriesDescription": "MT_OFF_-SAG", 
    "PartialFourier": 0.75, 
    "ConversionSoftwareVersion": "v1.0.20171204 (OpenJPEG build) GCC4.8.4", 
    "ShimSetting": [
        95, 
        -151, 
        197, 
        325, 
        391, 
        -24, 
        -168, 
        362
    ], 
    "PulseSequenceDetails": "%SiemensSeq%_gre", 
    "PatientPosition": "HFS", 
    "SequenceName": "_fl3d1", 
    "ReceiveCoilName": "32Ch_Head", 
    "ImageType": [
        "ORIGINAL", 
        "PRIMARY", 
        "M", 
        "ND"
    ], 
    "EchoTime": 0.011, 
    "SequenceVariant": "SP", 
    "PhaseResolution": 1, 
    "BaseResolution": 256, 
    "PixelBandwidth": 349, 
    "ScanOptions": "PFP", 
    "SoftwareVersions": "syngo_MR_B17", 
    "StationName": "MRC26121", 
    "Modality": "MR"
}
2

The problem here isn’t the suffix. _PD is ambiguous, so it’s preferred to use PDw for PD-weighted images and PDmap for quantitative proton density maps, but it’s permitted if you really want to preserve the ambiguity.

The validation problem is mt-on/mt-off, which is only permitted for the MPM, MTS and MTR suffixes (see Entity table - Magnetic Resonance Imaging).

Are these images part of a related sequence? If not, then, instead of mt-<on|off>, I would suggest something like acq-MTon and acq-MToff or similar.

cc @agahkarakuzu, in case you have thoughts on this situation.

1 Like
3

thanx a lot!
changing to acq-MTon/off helped