Json file is not so completed as dcmstak command #58
Comments
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@satra, Actually, I did not use --minmeta, still we lost a lot of information. |
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@satra I saw your former script here: https://gist.github.com/satra/8701942 |
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@anbai106 - we still use dicomstack internally for the metadata. i am a little surprised that you do not get the full metadata. is there anyway you can share some subset of dicom for us to test? also can you use the docker image for heudiconv to test? (https://hub.docker.com/r/nipy/heudiconv/) |
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@satra I will talk to the data owner and see if we can share one subject of dicom for each machine with you privately. |
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@anbai106 the first JSON file you list is the BIDS json header created by dcm2niix. The second output is the full DICOM header from dcmstack. The BIDS header does contain specific BIDS details that are generic to vendor (e.g. PhaseEncodingDirection in i,j,k space) while the DICOM includes many vendor specific details. Perhaps both can be saved, but the full DICOM header is not a valid BIDS json. |
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I have a similar problem with the JSON file. I'm using the latest dcm2niix/heudiconv and convert Siemens DICOM data. |
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@EdSplendor I would not call this a dcm2niix problem. dcm2niix is intentionally creating a BIDS-compatible JSON sidecar. In contrast, dcmstack is dumping all the DICOM tags into a JSON file that is not BIDS-compatible. While preserving details of the CSA header might be useful for your application, it is out of scope for dcm2niix. If dcm2niix is not capturing BIDS tags, it might be worth describing them to that they can be added to dcm2niix BIDS support. |
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I'd like to apologize for the phrasing I used. But you might be able to shed some light on the issue: |
Hi, thanks for your work, really helps me a lot
I have a question about the json file, the information in your json file is not completed compared with the json file from dcmstack(in your pipeline, you also use dcmstack niftiwrapper to get the metadata), So i want to ask why you just keep part of information of the metadata?
I know that for dcmstack, they dont work for Philips machine, the reason why you keep just this metadata is because of this? So for heudiconv, it is stable for all the machines or not? Philips, Siemens, GE???
Here is the result that i used heudiconv and dcmstack to get the jsons:
heudiconv:
{ "Manufacturer": "Siemens", "ManufacturersModelName": "Prisma_fit", "ProcedureStepDescription": "PRISMA_PREV_DEMALS", "ScanningSequence": "EP", "SequenceVariant": "SK_SP", "SeriesDescription": "ep2d_diff_FREE68_p2FAD_2.5mm_iso", "BodyPartExamined": "BRAIN", "ProtocolName": "ep2d_diff_FREE68_p2FAD_2.5mm_iso", "SequenceName": "_ep_b0", "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND"], "AcquisitionDateTime": "2015-10-08T16:36:36.362500", "MagneticFieldStrength": 3, "FlipAngle": 90, "EchoTime": 0.09, "RepetitionTime": 7.3, "EffectiveEchoSpacing": 0.000360002, "PhaseEncodingDirection": "j-", "ConversionSoftware": "dcm2niix", "ConversionSoftwareVersion": "v1.0.20170411 GCC4.8.4" }#################
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dcmstack
{ "global": { "const": { "SpecificCharacterSet": "ISO_IR 100", "ImageType": [ "ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND" ], "StudyTime": "161446.658000", "SeriesTime": "163643.455000", "AccessionNumber": "", "Modality": "MR", "Manufacturer": "SIEMENS", "SeriesDescription": "ep2d_diff_FREE68_p2FAD_2.5mm_iso", "ManufacturerModelName": "Prisma_fit", "BodyPartExamined": "BRAIN", "ScanningSequence": "EP", "SequenceVariant": [ "SK", "SP" ], "ScanOptions": "FS", "MRAcquisitionType": "2D", "AngioFlag": "N", "SliceThickness": 2.5, "RepetitionTime": 7300.0, "EchoTime": 90.0, "NumberOfAverages": 1.0, "ImagingFrequency": 123.252999, "ImagedNucleus": "1H", "EchoNumbers": 1, "MagneticFieldStrength": 3.0, "SpacingBetweenSlices": 2.5, "NumberOfPhaseEncodingSteps": 95, "EchoTrainLength": 47, "PercentSampling": 100.0, "PercentPhaseFieldOfView": 100.0, "PixelBandwidth": 1580.0, "SoftwareVersions": "syngo MR D13D", "ProtocolName": "ep2d_diff_FREE68_p2FAD_2.5mm_iso", "TimeOfLastCalibration": [ "123723.000000", "123723.000000" ], "TransmitCoilName": "Body", "AcquisitionMatrix": [ 96, 0, 0, 96 ], "InPlanePhaseEncodingDirection": "COL", "FlipAngle": 90.0, "VariableFlipAngleFlag": "N", "SAR": 0.31044795430682, "dBdt": 0.0, "StudyID": "1", "SeriesNumber": 8, "ImageOrientationPatient": [ 1.0, 0.0, 0.0, 0.0, 0.97591675922037, -0.2181432535579 ], "PositionReferenceIndicator": "", "SamplesPerPixel": 1, "PhotometricInterpretation": "MONOCHROME2", "Rows": 96, "Columns": 96, "PixelSpacing": [ 2.5, 2.5 ], "BitsAllocated": 16, "BitsStored": 12, "HighBit": 11, "PixelRepresentation": 0, "SmallestImagePixelValue": 0, "WindowCenterWidthExplanation": "Algo1", "PerformedProcedureStepStartTime": "161446.713000", "CsaImage.UsedChannelString": "XXXXXXXXXXXXXXXXXXXX", "CsaImage.MeasuredFourierLines": 0, "CsaImage.ImaPATModeText": "p2", "CsaImage.AcquisitionMatrixText": "96*96", "CsaImage.EchoLinePosition": 48, "CsaImage.BandwidthPerPixelPhaseEncode": 28.935, "CsaImage.RFSWDDataType": "predicted", "CsaImage.ImaRelTablePosition": [ 0, 0, 0 ], "CsaImage.PhaseEncodingDirectionPositive": 1, "CsaImage.SequenceMask": 134217732, "CsaImage.EchoPartitionPosition": 32, "CsaImage.NonPlanarImage": 0, "CsaImage.GSWDDataType": "predicted", "CsaImage.MultistepIndex": 0, "CsaImage.ImaAbsTablePosition": [ 0, 0, -1279 ], "CsaImage.RealDwellTime": 3300, "CsaImage.ImaCoilString": "HE1-4;NE1,2", "CsaImage.EchoColumnPosition": 48, "CsaImage.ImageType4MF": [ "ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "", "" ], "CsaImage.ImageHistory": [ "ChannelMixing:ND=true_CMM=1_CDM=1", "ACC1", "", "", "", "" ], "CsaSeries.Laterality4MF": "U", "CsaSeries.TalesReferencePower": 1121.60244, "CsaSeries.Operation_mode_flag": 0, "CsaSeries.dBdt_thresh": 0.0, "CsaSeries.ProtocolChangeHistory": 0, "CsaSeries.GradientDelayTime": [ 36.0, 35.0, 31.0 ], "CsaSeries.SARMostCriticalAspect": [ 5.33599974, 2.2896638, 0.0 ], "CsaSeries.B1rms": [ 7.07106781, 1.69914282 ], "CsaSeries.PATModeText": "p2", "CsaSeries.RelTablePosition": [ 0, 0, 0 ], "CsaSeries.NumberOfPrescans": 0, "CsaSeries.dBdt_limit": 0.0, "CsaSeries.Stim_lim": [ 42.70069885, 23.97319984, 36.48099899 ], "CsaSeries.PatReinPattern": "1;HFS;50.00;62.00;1;0;0;-397572668", "CsaSeries.B1rmsSupervision": "NO", "CsaSeries.PhaseSliceOversampling": "NONE", "CsaSeries.ReadoutGradientAmplitude": 0.0, "CsaSeries.MrProtocolVersion": 41340006, "CsaSeries.RFSWDMostCriticalAspect": "Bore Local", "CsaSeries.SequenceFileOwner": "SIEMENS", "CsaSeries.GradientMode": "Fast*", "CsaSeries.EchoTrainLength": 47, "CsaSeries.SliceArrayConcatenations": 1, "CsaSeries.FlowCompensation": "No", "CsaSeries.TransmitterCalibration": 254.388132, "CsaSeries.Isocentered": 0, "CsaSeries.AbsTablePosition": -1279, "CsaSeries.ReadoutOS": 2.0, "CsaSeries.dBdt_max": 0.0, "CsaSeries.RFSWDOperationMode": 0, "CsaSeries.SelectionGradientAmplitude": 0.0, "CsaSeries.PhaseGradientAmplitude": 0.0, "CsaSeries.RfWatchdogMask": 0, "CsaSeries.CoilForGradient2": "AS82", "CsaSeries.Stim_mon_mode": 2, "CsaSeries.CoilId": [ 255, 0, 0, 0, 0, 4868, 4867, 0, 0, 0, 0 ], "CsaSeries.Stim_max_ges_norm_online": 0.62531626, "CsaSeries.CoilString": "HE1-4;NE1,2", "CsaSeries.CoilForGradient": "void", "CsaSeries.DICOMAcquisitionContrast": "", "CsaSeries.TablePositionOrigin": [ 0, 0, -1279 ], "CsaSeries.MiscSequenceParam": [ 40, 68, 68, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 524288, 0, 0, 0, 0, 0, 2, 11128, 0, 0, 0, 0, 0, 0 ], "CsaSeries.SafetyStandard": "IEC", "CsaSeries.GradientEchoTrainLength": 47, "CsaSeries.LongModelName": "NUMARIS/4", "CsaSeries.DICOMImageFlavor": "", "CsaSeries.Stim_faktor": 1.0, "CsaSeries.SW_korr_faktor": 1.0, "CsaSeries.Sed": [ 1000000.0, 308.79541916, 308.79541916 ], "CsaSeries.PositivePCSDirections": "+LPH", "CsaSeries.SliceResolution": 1.0, "CsaSeries.Stim_max_online": [ 6.70691442, 3.44702697, 21.44870186 ], "CsaSeries.t_puls_max": 0.0, "CsaSeries.RFEchoTrainLength": 1, "CsaSeries.MrPhoenixProtocol.ulVersion": 41340006, "CsaSeries.MrPhoenixProtocol.tSequenceFileName": "%SiemensSeq%\\ep2d_diff", "CsaSeries.MrPhoenixProtocol.tProtocolName": "ep2d_diff_FREE68_p2FAD_2.5mm_iso", "CsaSeries.MrPhoenixProtocol.tdefaultEVAProt": "%SiemensEvaDefProt%\\DTI\\DTI.evp", "CsaSeries.MrPhoenixProtocol.tReferenceImage0": "1.3.12.2.1107.5.2.43.67048.2015100816151328731925230", "CsaSeries.MrPhoenixProtocol.tReferenceImage1": "1.3.12.2.1107.5.2.43.67048.2015100816151616715125234", "CsaSeries.MrPhoenixProtocol.tReferenceImage2": "1.3.12.2.1107.5.2.43.67048.201510081615194716725238", "CsaSeries.MrPhoenixProtocol.lScanRegionPosTra": 0.0, "CsaSeries.MrPhoenixProtocol.ucScanRegionPosValid": 1, "CsaSeries.MrPhoenixProtocol.lPtabAbsStartPosZ": -1279, "CsaSeries.MrPhoenixProtocol.bPtabAbsStartPosZValid": 1, "CsaSeries.MrPhoenixProtocol.ucTablePositioningMode": 1, "CsaSeries.MrPhoenixProtocol.ucEnableNoiseAdjust": 1, "CsaSeries.MrPhoenixProtocol.lContrasts": 1, "CsaSeries.MrPhoenixProtocol.lCombinedEchoes": 1, 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240.0,Really hope to hear from you:)
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