So I’m struggling to identify the slice timing order for one of our experiments which was done a few years ago.
The issue is that I cannot easily tell the slice order of the images when trying to do slice timing correction with fmriprep.
I have tried two ways to identify this information:
- 1: Using dcm2bids_helper to generate json files
the resulting file, however, does not contain slice timing info:
{
"Modality": "MR",
"MagneticFieldStrength": 3,
"ImagingFrequency": 127.748,
"Manufacturer": "Philips",
"ManufacturersModelName": "Ingenia",
"InstitutionName": "LMU Muenchen",
"InstitutionalDepartmentName": "MRT",
"DeviceSerialNumber": "42363",
"StationName": "radimr1m",
"BodyPartExamined": "HEAD",
"PatientPosition": "HFS",
"SoftwareVersions": "5.3.1\\5.3.1.0",
"MRAcquisitionType": "2D",
"SeriesDescription": "Resting",
"ProtocolName": "Resting",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"],
"SeriesNumber": 1201,
"AcquisitionTime": "22:03:7.760000",
"AcquisitionNumber": 12,
"PhilipsRescaleSlope": 0.788767,
"PhilipsRescaleIntercept": 0,
"PhilipsScaleSlope": 0.0794925,
"UsePhilipsFloatNotDisplayScaling": 1,
"SliceThickness": 3,
"SpacingBetweenSlices": 3,
"SAR": 0.13914,
"EchoTime": 0.03,
"RepetitionTime": 2.5,
"MTState": false,
"FlipAngle": 90,
"CoilString": "MULTI COIL",
"PercentPhaseFOV": 105.882,
"PercentSampling": 98.75,
"EchoTrainLength": 27,
"PhaseEncodingSteps": 80,
"AcquisitionMatrixPE": 80,
"ReconMatrixPE": 144,
"ParallelReductionFactorInPlane": 3,
"ParallelAcquisitionTechnique": "SENSE",
"WaterFatShift": 7.29209,
"EstimatedEffectiveEchoSpacing": 0.000113211,
"EstimatedTotalReadoutTime": 0.0161892,
"PixelBandwidth": 2079,
"PhaseEncodingAxis": "j",
"ImageOrientationPatientDICOM": [
1,
0,
0,
0,
1,
0 ],
"InPlanePhaseEncodingDirectionDICOM": "COL",
"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20220505"
}
- 2 I tried to use SPM’s DICOM import with metadata export. it does not contain slice order info as well.
{
"history": {
"procstep": {
"descrip": "dicom to nifti import",
"version": "spm_dicom_convert.m - version 7201 - SPM12 (7219)",
"procpar": []
},
"input": {
"filename": "AnonymousFileName",
"history": []
},
"output": {
"imtype": "ORIGINAL\\PRIMARY\\M_FFE\\M\\FFE",
"units": "a.u."
}
},
"acqpar": [
{
"FileMetaInformationGroupLength": 198,
"FileMetaInformationVersion": [0,1],
"MediaStorageSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
"MediaStorageSOPInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121420162329",
"TransferSyntaxUID": "1.2.840.10008.1.2.1",
"ImplementationClassUID": "1.3.46.670589.11.0.0.51.4.53.1",
"ImplementationVersionName": "Philips MR 53.1 ",
"SpecificCharacterSet": "ISO_IR 100",
"ImageType": "ORIGINAL\\PRIMARY\\M_FFE\\M\\FFE",
"InstanceCreationDate": 736928,
"InstanceCreationTime": 81249.53999999999,
"InstanceCreatorUID": "1.3.46.670589.11.89.5",
"SOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
"SOPInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121420162329",
"StudyDate": 736928,
"SeriesDate": 736928,
"AcquisitionDate": 736928,
"ContentDate": 736928,
"StudyTime": 75867,
"SeriesTime": 77991.71000000001,
"AcquisitionTime": 78064.25999999999,
"ContentTime": 78064.25999999999,
"Modality": "MR",
"Manufacturer": "Philips Healthcare",
"InstitutionName": "LMU Muenchen",
"StationName": "radimr1m",
"SeriesDescription": "Resting ",
"InstitutionalDepartmentName": "MRT ",
"ManufacturerModelName": "Ingenia ",
"ReferencedPerformedProcedureStepSequence": [
{
"InstanceCreationDate": 736928,
"InstanceCreationTime": 75867.54399999999,
"InstanceCreatorUID": "1.3.46.670589.11.89.5",
"ReferencedSOPClassUID": "1.2.840.10008.3.1.2.3.3",
"ReferencedSOPInstanceUID": "1.3.46.670589.11.42363.5.0.10568.2017082121042754001",
"InstanceNumber": 0,
"Private_2005_0014": "Philips MR Imaging DD 005 ",
"Private_2005_1404": 1,
"Private_2005_1406": 1
}
],
"ReferencedImageSequence": [
{
"ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
"ReferencedSOPInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121234342003"
},
{
"ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
"ReferencedSOPInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121234342003"
},
{
"ReferencedSOPClassUID": "1.2.840.10008.5.1.4.1.1.4",
"ReferencedSOPInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121234345007"
}
],
"PatientName": "Anonymous",
"PatientID": "2323453 ",
"PatientSex": "M ",
"PatientAge": 47.6,
"PatientWeight": 70,
"PregnancyStatus": 1,
"BodyPartExamined": "HEAD",
"ScanningSequence": "GR",
"SequenceVariant": "SK",
"ScanOptions": "FS",
"MRAcquisitionType": "2D",
"SliceThickness": 3,
"RepetitionTime": 2500.0009765625,
"EchoTime": 30,
"NumberOfAverages": 1,
"ImagingFrequency": 127.747823,
"ImagedNucleus": "1H",
"EchoNumbers": 1,
"MagneticFieldStrength": 3,
"SpacingBetweenSlices": 3,
"NumberOfPhaseEncodingSteps": 80,
"EchoTrainLength": 27,
"PercentSampling": 98.75,
"PercentPhaseFieldOfView": 105.882358551025,
"PixelBandwidth": 2079,
"DeviceSerialNumber": "42363 ",
"SoftwareVersions": "5.3.1\\5.3.1.0 ",
"ProtocolName": "Resting ",
"TriggerTime": 7500,
"LowRRValue": 0,
"HighRRValue": 0,
"IntervalsAcquired": 0,
"IntervalsRejected": 0,
"HeartRate": 0,
"ReconstructionDiameter": 237,
"ReceiveCoilName": "MULTI COIL",
"AcquisitionMatrix": [80,0,0,80],
"InPlanePhaseEncodingDirection": "COL ",
"FlipAngle": 90,
"SAR": 0.13913993537425,
"dBdt": 124.829917907714,
"Tag_0018_1320": 1.433357357978821,
"PatientPosition": "HFS ",
"AcquisitionDuration": 459.9490051269531,
"DiffusionBValue": 0,
"DiffusionGradientOrientation": [0,0,0],
"StudyInstanceUID": "1.3.46.670589.11.42363.5.0.10568.2017082121042713000",
"SeriesInstanceUID": "1.3.46.670589.11.42363.5.0.4596.2017082121395174275",
"StudyID": "537995066 ",
"SeriesNumber": 501,
"AcquisitionNumber": 5,
"InstanceNumber": 4,
"ImagePositionPatient": [-117.76470738649,-119.76871234178,-36.932861328125],
"ImageOrientationPatient": [1,0,0,0,1,0],
"FrameOfReferenceUID": "1.3.46.670589.11.42363.5.0.3400.2017082121212508000",
"TemporalPositionIdentifier": 4,
"NumberOfTemporalPositions": 180,
"SliceLocation": 36.932861328125,
"SamplesPerPixel": 1,
"PhotometricInterpretation": "MONOCHROME2 ",
"Rows": 144,
"Columns": 144,
"PixelSpacing": [1.64705884456634,1.64705884456634],
"BitsAllocated": 16,
"BitsStored": 12,
"HighBit": 11,
"PixelRepresentation": 0,
"WindowCenter": 1473,
"WindowWidth": 2561,
"RescaleIntercept": 0,
"RescaleSlope": 0.8021978021978,
"RescaleType": "normalized",
"PerformedStationAETitle": "RADIMR1M",
"PerformedProcedureStepStartDate": 736928,
"PerformedProcedureStepStartTime": 75867,
"PerformedProcedureStepEndDate": 736928,
"PerformedProcedureStepEndTime": 75867,
"PerformedProcedureStepID": "537995066 ",
"PerformedProtocolCodeSequence": [
{
"CodeValue": "UNDEFINED ",
"CodingSchemeDesignator": "UNDEFINED ",
"CodeMeaning": "UNDEFINED ",
"ContextGroupExtensionFlag": "N "
}
],
"IssueDateOfImagingServiceRequest": 736928,
"IssueTimeOfImagingServiceRequest": 75867.13800000001,
"PrivateCreatorGroup2001": "Philips Imaging DD 001",
"Private_2001_0011": "Philips Imaging DD 002",
"ChemicalShift": 0,
"ChemicalShiftNumberMR": 0,
"DiffusionBFactor": 0,
"ImageEnhanced": "N ",
"ImageTypeEDES": "U ",
"PhaseNumber": 1,
"Private_2001_1009": 0,
"SliceNumberMR": 1,
"SliceOrientation": "TRANSVERSAL ",
"Private_2001_100c": "N ",
"Private_2001_100e": "N ",
"Private_2001_100f": 0,
"Private_2001_1010": "NO",
"DiffusionEchoTime": 0,
"DynamicSeries": "Y ",
"EPIFactor": 27,
"NumberofEchoes": 1,
"NumberofLocations": 1,
"NumberofPCDirections": 0,
"NumberofPhasesMRAttributeName": 1,
"NumberofSlicesMR": 48,
"PartialMatrixScanned": "N ",
"PCVelocity": [0,0,0],
"PrepulseDelay": 0,
"PrepulseType": "NO",
"ReconstructionNumberMR": 1,
"RespirationSync": "NO",
"Private_2001_1020": "FEEPI ",
"SPIR": "Y ",
"WaterFatShift": 7.292090892791748,
"Private_2001_1023": 90,
"Private_2001_1024": "N ",
"Private_2001_1025": "30",
"StackSequence": [
{
"PrivateCreatorGroup2001": "Philips Imaging DD 001",
"NumberofStackSlices": 48,
"StackRadialAngle": 0,
"StackRadialAxis": "AP",
"StackSliceNumber": 1,
"StackType": "PARALLEL",
"PrivateCreatorGroup2005": "Philips MR Imaging DD 001 ",
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"Private_2005_1081": "FH",
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}
],
"NumberofStacks": 1,
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"Private_2001_1063": "ELSEWHERE ",
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"NumberofDynamicScans": 180,
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"Private_2001_1087": "1H",
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"Private_2005_0012": "Philips MR Imaging DD 003 ",
"Private_2005_0013": "Philips MR Imaging DD 004 ",
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"NumberofChemicalShifts": 0,
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"Private_2005_1327": "REAL",
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"VolumetricProperties": "VOLUME",
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