Hi there,
Apologies for the basic question, asking because I can’t find the answer. I’ve got a bunch of scans (dwi and func at different resolutions) for many subjects and many sessions, and many fieldmaps for each sub/session. I’m trying to put the IntendedFor() field in my .json sidecars. My first question is,
-
how do I know which fieldmaps should be applied to which session? What are the rules, and what is the minimum that matches between two files to make them compatible? I know the acquisition time of the fieldmaps should be before the acquisition time of the scan, but other than that, I don’t know.
-
Secondly, do i have to do some kind of conversion on the real&imaginary fmaps, or can I just use the ‘e1’ or ‘e2’ (normal) version and disregard ‘e2_imaginary’ ‘e2_real’ ?
-
Do I put intendedfor in magnitude1/2 and phasediff files? Does a run need to be assigned a magnitude1, 2 and phasediff to be accurately undistorted, or if it just matched one file, is that still valid?
If it helps, I’ve put the metadata labels of the data available in my .jsons to see what possible filters I could use in determining matching runs.
Each session has these file types, listed below:
fmap
- magnitude1
- e1
- real
- imaginary
- magnitude2
- e2
- real
- imginary
- phasediff
func
- high res rest
- low res rest
dwi
- high res b1000
- high res b10002500
- low res b1000
- low res b10002500
Thank you in advance for any help!
Kaley
JSON FILES: Bold, magnitude, phasediff
func bold .json
{
"AcquisitionMatrixPE":
"AcquisitionNumber":
"AcquisitionTime":
"BandwidthPerPixelPhaseEncode":
"BaseResolution":
"BidsGuess": [
"func",
"_acq-epfid2_dir-AP_run-7_bold"
],
"CoilCombinationMethod":
"ConversionSoftware":
"ConversionSoftwareVersion":
"DerivedVendorReportedEchoSpacing": ,
"DeviceSerialNumber":
"DwellTime":
"EchoTime":
"EffectiveEchoSpacing":
"FlipAngle":
"ImageOrientationPatientDICOM":
"ImageType":
"ImagingFrequency":
"InPlanePhaseEncodingDirectionDICOM":
"InstitutionName":
"MRAcquisitionType":
"MagneticFieldStrength":
"Manufacturer":
"ManufacturersModelName":
"MatrixCoilMode":
"Modality":
"NonlinearGradientCorrection":,
"PartialFourier":
"PatientPosition":
"PercentPhaseFOV":
"PercentSampling":
"PhaseEncodingDirection":
"PhaseEncodingSteps":
"PhaseResolution":
"PixelBandwidth":
"ProtocolName": "ep2d_bold_2.5TR_3.5mm",
"PulseSequenceDetails": ,
"ReceiveCoilName":
"ReconMatrixPE":
"RepetitionTime":
"SAR":
"ScanOptions":
"ScanningSequence":
"SequenceName":
"SequenceVariant":
"SeriesDescription": "ep2d_bold_2.5TR_3.5mm",
"SeriesNumber"
"ShimSetting":
"SliceThickness":
"SliceTiming":
"SoftwareVersions": "
"SpacingBetweenSlices"
"TaskName":
"TotalReadoutTime":
"TxRefAmp":
}
fmap magnitude2 .json
{
"AcquisitionMatrixPE":
"AcquisitionNumber":
"AcquisitionTime":
"BaseResolution":
"BidsGuess": [
"fmap",
"_acq-fm2_magnitude2"
],
"CoilCombinationMethod":
"ConversionSoftware":
"ConversionSoftwareVersion":
"DeviceSerialNumber":
"DwellTime":
"EchoNumber":
"EchoTime":
"FlipAngle":
"ImageOrientationPatientDICOM":
"ImageType":
"ImagingFrequency":
"InPlanePhaseEncodingDirectionDICOM":
"InstitutionName":
"IntendedFor":
"MRAcquisitionType
"MagneticFieldStrength"
"Manufacturer":
"ManufacturersModelName":
"MatrixCoilMode":
"Modality":
"MultibandAccelerationFactor":
"NonlinearGradientCorrection":
"PartialFourier":
"PatientPosition":
"PercentPhaseFOV":
"PercentSampling":
"PhaseEncodingDirection":
"PhaseEncodingSteps":
"PhaseResolution":
"PixelBandwidth": ,
"ProtocolName": "FieldMap_2mm",
"PulseSequenceDetails":
"ReceiveCoilName":
"ReconMatrixPE":
"RepetitionTime": ,
"SAR":
"ScanningSequence":
"SequenceName":
"SequenceVariant":
"SeriesDescription": "FieldMap_2mm",
"SeriesNumber":
"ShimSetting":
"SliceThickness":
"SliceTiming":
"SoftwareVersions":
"SpacingBetweenSlices":
"TxRefAmp":
}
fmap phasediff .json
{
"AcquisitionMatrixPE":
"AcquisitionNumber":
"AcquisitionTime":
"CoilString": ,
"ConversionSoftware":,
"ConversionSoftwareVersion":
"DeviceSerialNumber": "",
"EchoNumber":
"EchoTime":
"FlipAngle":,
"ImageOrientationPatientDICOM":
"ImageType":
"ImagingFrequency": ,
"InPlanePhaseEncodingDirectionDICOM": "",
"InstitutionName": "",
"IntendedFor":
"MRAcquisitionType": "",
"MagneticFieldStrength":
"Manufacturer": "",
"ManufacturersModelName": "",
"Modality": "",
"PatientPosition": "",
"PercentPhaseFOV":
"PercentSampling":
"PhaseEncodingAxis":
"PixelBandwidth":
"ProtocolName": "
"ReconMatrixPE":
"RepetitionTime":
"SAR":
"ScanOptions":
"ScanningSequence": "
"SequenceVariant":
"SeriesDescription": "FieldMap_2mm",
"SeriesNumber":
"ShimSetting":
],
"SliceThickness":
"SoftwareVersions":
"SpacingBetweenSlices"
"SpoilingState":
}