Bids fmap question--Direct fieldmapping?

,
1

Hi all,

I’m trying to determine what case of field map this is. When I run direct dcm2niix I get this

image

The scanner is Phillips.

Is this Case 3 direct field mapping in which instance the nii.gz and .json files will be named magnitude.json and magnitude.nii.gz and the fieldmaphz.nii.gz and fieldmaphz.json files will be named fieldmap.json and fieldmap.nii.gz.

https://bids-specification.readthedocs.io/en/stable/modality-specific-files/magnetic-resonance-imaging-data.html#case-3-direct-field-mapping

Also separate question–I noticed that the dir-{label} is not allowed in this instance? Why is that? Would it be best just to do acq-B0mapAP? How do I specify directionality if dir label is not allowed?

Thanks.

–Subbi M.

2

(edited fixed below)

3

@Steven

This is the .json file for AP_801_e1.json


{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 127.748,
	"Manufacturer": "Philips",
	"ManufacturersModelName": "Ingenia Elition X",
	"InstitutionName": "Albert Einstein College",
	"InstitutionalDepartmentName": "MRI",
	"DeviceSerialNumber": "45055",
	"StationName": "MMCMRCMR001",
	"BodyPartExamined": "BRAIN",
	"PatientPosition": "HFS",
	"SoftwareVersions": "5.9.0\\5.9.0.0",
	"MRAcquisitionType": "3D",
	"SeriesDescription": "104E_B0 map-AP",
	"ProtocolName": "104E_B0 map-AP",
	"ScanningSequence": "RM",
	"SequenceVariant": "SP",
	"ScanOptions": "FS",
	"PulseSequenceName": "T1FFE",
	"ImageType": ["ORIGINAL", "PRIMARY", "T1", "MIXED", "FIELDMAPHZ"],
	"SeriesNumber": 801,
	"AcquisitionTime": "11:45:27.580000",
	"AcquisitionNumber": 8,
	"PhilipsRWVSlope": 1.24274,
	"PhilipsRWVIntercept": 0,
	"PhilipsRescaleSlope": 1.24274,
	"PhilipsRescaleIntercept": 0,
	"PhilipsScaleSlope": 0.000238808,
	"UsePhilipsFloatNotDisplayScaling": 1,
	"SliceThickness": 3,
	"SpacingBetweenSlices": 3,
	"EchoNumber": 1,
	"EchoTime": 0.00251,
	"RepetitionTime": 0.026,
	"MTState": false,
	"SpoilingState": true,
	"SpoilingType": "COMBINED",
	"FlipAngle": 26,
	"CoilString": "MULTI COIL",
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"PhaseEncodingSteps": 80,
	"AcquisitionMatrixPE": 80,
	"ReconMatrixPE": 80,
	"ParallelReductionFactorInPlane": 2,
	"ParallelAcquisitionTechnique": "SENSE",
	"ParallelReductionOutOfPlane": 2,
	"WaterFatShift": 0.99794,
	"EstimatedEffectiveEchoSpacing": 1.45417e-05,
	"EstimatedTotalReadoutTime": 0.0011488,
	"AcquisitionDuration": 102.024,
	"PixelBandwidth": 435.237,
	"ImageOrientationPatientDICOM": [
		0.997935,
		0.00933612,
		0.0635505,
		-0.00943617,
		0.999955,
		0.00127432	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20220720"
}
4

Hi @Steven,

How would you BIDS name these files?

Thanks.

–Subbi M.

5

(edited fixed below)

6

Hi @Steven ,

Does the image type “ImageType”: [“ORIGINAL”, “PRIMARY”, “T1”, “MIXED”, “FIELDMAPHZ”],
determine what Case.

I’m confused how to determine between Case 1 and Case 3 since the file has fieldmaphz in the name.

Thanks.

–Subbi M.

7

What about the e2 json? That could indicate Case 3 in which case name like Magnetic Resonance Imaging - Brain Imaging Data Structure 1.10.0

sub-<label>/
    [ses-<label>/]
        fmap/
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>][_chunk-<index>]_fieldmap.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>][_chunk-<index>]_fieldmap.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>][_chunk-<index>]_magnitude.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>][_chunk-<index>]_magnitude.nii[.gz]

and make sure the unit field in the json is filled out, as described in the BIDS specification.

That field is only relevant for PEPOLAR fieldmaps, since reverse phase encoded pairs are used to make the map.

1 Like
8

Hi,

This is the .json file for 801_e2_fieldmaphz.json

{
	"Modality": "MR",
	"MagneticFieldStrength": 3,
	"ImagingFrequency": 127.748,
	"Manufacturer": "Philips",
	"ManufacturersModelName": "Ingenia Elition X",
	"InstitutionName": "Albert Einstein College",
	"InstitutionalDepartmentName": "MRI",
	"DeviceSerialNumber": "45055",
	"StationName": "MMCMRCMR001",
	"BodyPartExamined": "BRAIN",
	"PatientPosition": "HFS",
	"SoftwareVersions": "5.9.0\\5.9.0.0",
	"MRAcquisitionType": "3D",
	"SeriesDescription": "104E_B0 map-AP",
	"ProtocolName": "104E_B0 map-AP",
	"ScanningSequence": "RM",
	"SequenceVariant": "SP",
	"ScanOptions": "FS",
	"PulseSequenceName": "T1FFE",
	"ImageType": ["ORIGINAL", "PRIMARY", "T1", "MIXED", "REAL", "FIELDMAPHZ"],
	"SeriesNumber": 801,
	"AcquisitionTime": "11:45:27.580000",
	"AcquisitionNumber": 8,
	"PhilipsRWVSlope": 0.105983,
	"PhilipsRWVIntercept": -217,
	"PhilipsRescaleSlope": 0.105983,
	"PhilipsRescaleIntercept": -217,
	"PhilipsScaleSlope": 9.4185,
	"UsePhilipsFloatNotDisplayScaling": 1,
	"Units": "Hz",
	"SliceThickness": 3,
	"SpacingBetweenSlices": 3,
	"EchoNumber": 2,
	"RepetitionTime": 0.026,
	"MTState": false,
	"SpoilingState": true,
	"SpoilingType": "COMBINED",
	"FlipAngle": 26,
	"CoilString": "MULTI COIL",
	"PercentPhaseFOV": 100,
	"PercentSampling": 100,
	"PhaseEncodingSteps": 80,
	"AcquisitionMatrixPE": 80,
	"ReconMatrixPE": 80,
	"ParallelReductionFactorInPlane": 2,
	"ParallelAcquisitionTechnique": "SENSE",
	"ParallelReductionOutOfPlane": 2,
	"WaterFatShift": 0.99794,
	"EstimatedEffectiveEchoSpacing": 1.45417e-05,
	"EstimatedTotalReadoutTime": 0.0011488,
	"AcquisitionDuration": 102.024,
	"PixelBandwidth": 435.237,
	"ImageOrientationPatientDICOM": [
		0.997935,
		0.00933612,
		0.0635505,
		-0.00943617,
		0.999955,
		0.00127432	],
	"InPlanePhaseEncodingDirectionDICOM": "COL",
	"ConversionSoftware": "dcm2niix",
	"ConversionSoftwareVersion": "v1.0.20220720"
}
9

Hi @Steven,

I think Case 3 because of this “ImageType”: [“ORIGINAL”, “PRIMARY”, “T1”, “MIXED”, “REAL”, “FIELDMAPHZ”],

But not sure. Have only worked with Case 4 before.

Is it Case 1 or Case 3?

Thanks.

–Subbi M.

10

I would think case 3

1 Like
11

Hi @Steven ,

Thanks. Will do ahead and name accordingly to Case 3 BIDS convention.

–Subbi M.