Dear humans!
I am running BIDS validation on Healthy Brain Network (HBN) MRI data.
Data from site ‘SI’ structured as:
fmap/
sub-[_ses-][_acq-][_run-]_phasediff.nii[.gz]
sub-[_ses-][_acq-][_run-]_phasediff.json
sub-[_ses-][_acq-][_run-]_magnitude1.nii[.gz]
sub-[_ses-][_acq-][_run-]_magnitude2.nii[.gz]
sub-[_ses-][_acq-][_run-]_magnitude1.json
sub-[_ses-][_acq-][_run-]_magnitude2json
throws an error for _phasediff.json files:
[ERR] You have to define ‘EchoTime1’ and ‘EchoTime2’ for this file. (code: 15 - ECHO_TIME1-2_NOT_DEFINED)
Here’s _phasediff.json example content:
{
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ProcedureStepDescription": "CMI_HBN",
"DeviceSerialNumber": "26121",
"AcquisitionMatrixPE": 64,
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
0
],
"ManufacturersModelName": "Avanto",
"ProtocolName": "Field_Map",
"RepetitionTime": 0.492,
"MagneticFieldStrength": 1.5,
"PhaseEncodingSteps": 64,
"MRAcquisitionType": "2D",
"SliceThickness": 3,
"DwellTime": 3e-05,
"TxRefAmp": 236.302,
"PixelBandwidth": 260,
"SAR": 0.360405,
"ConversionSoftware": "dcm2niix",
"ScanningSequence": "GR",
"Manufacturer": "Siemens",
"PercentPhaseFOV": 100,
"ReconMatrixPE": 64,
"FlipAngle": 90,
"SeriesDescription": "Field_Map",
"PartialFourier": 1,
"ConversionSoftwareVersion": "v1.0.20171204 (OpenJPEG build) GCC4.8.4",
"ShimSetting": [
124,
-198,
437,
1256,
257,
550,
668,
346
],
"PulseSequenceDetails": "%SiemensSeq%_gre_field_mapping",
"PatientPosition": "HFS",
"SequenceName": "_fm2d2r",
"ReceiveCoilName": "32Ch_Head",
"SpacingBetweenSlices": 3,
"ImageType": [
"ORIGINAL",
"PRIMARY",
"P",
"ND"
],
"EchoTime": 0.00804,
"SequenceVariant": "SP",
"PhaseResolution": 1,
"BaseResolution": 64,
"PhaseEncodingDirection": "j-",
"SoftwareVersions": "syngo_MR_B17",
"StationName": "MRC26121",
"Modality": "MR",
"EchoNumber": 2
}
EchoTime in _magnitude1.json =0.00328 ,and in _magnitude2.json = 0.00804
According to the BIDS website:
Does this mean that for _phasediff.json EchoTime1=0.00328 and EchoTime2= 0.00804?