I’m trying to compute SUV values for my FET-PET images, however it throws the following error:
Geometric issues were found with 1 of the series. Please use caution.
Traceback (most recent call last):
File "C:\Users\kated\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMUtils.py", line 678, in getLoadablesFromFileLists
loadablesByPlugin[plugin] = plugin.examine(fileLists)
File "C:/Users/kated/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules/DICOMPETSUVPlugin.py", line 127, in examine
rwvmFile = self.generateRWVMforFileList(fileList)
File "C:/Users/kated/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules/DICOMPETSUVPlugin.py", line 169, in generateRWVMforFileList
raise RuntimeError("SUVFactorCalculator CLI did not complete cleanly")
RuntimeError: SUVFactorCalculator CLI did not complete cleanly
DICOM Plugin failed: SUVFactorCalculator CLI did not complete cleanly
Traceback (most recent call last):
File "C:\Users\kated\AppData\Local\NA-MIC\Slicer 4.11.20210226\lib\Slicer-4.11\qt-scripted-modules\DICOMLib\DICOMUtils.py", line 678, in getLoadablesFromFileLists
loadablesByPlugin[plugin] = plugin.examine(fileLists)
File "C:/Users/kated/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules/DICOMPETSUVPlugin.py", line 127, in examine
rwvmFile = self.generateRWVMforFileList(fileList)
File "C:/Users/kated/AppData/Local/NA-MIC/Slicer 4.11.20210226/NA-MIC/Extensions-29738/PETDICOMExtension/lib/Slicer-4.11/qt-scripted-modules/DICOMPETSUVPlugin.py", line 169, in generateRWVMforFileList
raise RuntimeError("SUVFactorCalculator CLI did not complete cleanly")
RuntimeError: SUVFactorCalculator CLI did not complete cleanly
DICOM Plugin failed: SUVFactorCalculator CLI did not complete cleanly
This issue seemed similar to Unnamed Series as a Scalar Volume - #4 by lassoan
Here, the advice was to check that certain values in the metadata we’re not ruined by anonimization.
However, I can’t find the following attributes in my metadata: injectedDose, patientWeight, , injectionTime, radionuclideHalfLife. I was wondering what I’m doing wrong here?
I obtain the metadata by right-clicking on the patient file → “View metadata”. The metadata looks as follows:
[0008,0005] SpecificCharacterSet ISO_IR 100 CS 10
[0008,0008] ImageType [2] ORIGINAL, PRIMARY CS 16
[0008,0016] SOPClassUID 1.2.840.10008.5.1.4.1.1.128 UI 28
[0008,0018] SOPInstanceUID 1.2.19.99.170800 UI 16
[0008,0020] StudyDate 20120327 DA 8
[0008,0021] SeriesDate 20120327 DA 8
[0008,0022] AcquisitionDate 20120327 DA 8
[0008,0023] ContentDate 20120327 DA 8
[0008,0030] StudyTime 125233.525000 TM 14
[0008,0031] SeriesTime 131012.000000 TM 14
[0008,0032] AcquisitionTime 133012.000000 TM 14
[0008,0033] ContentTime 135930.000000 TM 14
[0008,0050] AccessionNumber A4766GLIMAS SH 12
[0008,0060] Modality PT CS 2
[0008,0070] Manufacturer Manu LO 4
[0008,0080] InstitutionName Institute of Radiology LO 22
[0008,0081] InstitutionAddress Dept of Radiology ST 18
[0008,0090] ReferringPhysicianName PN 0
[0008,0092] ReferringPhysicianAddress ST 0
[0008,1010] StationName TOESTEL SH 8
[0008,1030] StudyDescription TheStudy LO 8
[0008,103e] SeriesDescription FET Brain Corr Sum 20-40 UHD LO 28
[0008,1050] PerformingPhysicianName PN 0
[0008,1060] NameOfPhysiciansReadingStudy PN 0
[0008,1070] OperatorsName PN 0
[0008,1090] ManufacturerModelName model LO 6
[0008,1110] ReferencedStudySequence SQ 98
[fffe,e000] Item na 82
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.3.1.2.3.1 UI 24
[0008,1155] ReferencedSOPInstanceUID 1.3.51.0.1.1.140.140.21.70.2684395.2684374 UI 42
[0008,1120] ReferencedPatientSequence SQ 114
[fffe,e000] Item na 98
[0008,1150] ReferencedSOPClassUID 1.2.840.10008.3.1.2.1.1 UI 24
[0008,1155] ReferencedSOPInstanceUID 1.2.124.113532.59449.13802.32934.20200805.164135.224473808 UI 58
[0008,1250] RelatedSeriesSequence SQ 392
[fffe,e000] Item na 376
[0020,000d] StudyInstanceUID 1.3.51.0.1.1.140.140.21.70.2684395.2684374 UI 42
[0020,000e] SeriesInstanceUID 1.3.12.2.1107.5.1.4.31082.30000021051205564447000012755 UI 56
[0040,a170] PurposeOfReferenceCodeSequence SQ 246
[fffe,e000] Item na 100
[0008,0100] CodeValue 122401 SH 6
[0008,0102] CodingSchemeDesignator DCM SH 4
[0008,0104] CodeMeaning Same Anatomy LO 12
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20030619000000.000000 DT 22
[0008,010f] ContextIdentifier 7210 CS 4
[fffe,e000] Item na 114
[0008,0100] CodeValue 122403 SH 6
[0008,0102] CodingSchemeDesignator DCM SH 4
[0008,0104] CodeMeaning For Attenuation Correction LO 26
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20030619000000.000000 DT 22
[0008,010f] ContextIdentifier 7210 CS 4
[0010,0010] PatientName PGLIMAS0001 PN 12
[0010,0020] PatientID PGLIMAS0001 LO 12
[0010,0021] IssuerOfPatientID UNKNOWN LO 8
[0010,0030] PatientBirthDate 19570119 DA 8
[0010,0032] PatientBirthTime 000000.000000 TM 14
[0010,0040] PatientSex M CS 2
[0010,1000] RETIRED_OtherPatientIDs "" LO 2
[0010,1001] OtherPatientNames "" PN 2
[0010,1080] MilitaryRank "" LO 2
[0010,21b0] AdditionalPatientHistory "" LT 2
[0018,0022] ScanOptions TEST CS 4
[0018,0050] SliceThickness 3 DS 2
[0018,1000] DeviceSerialNumber 31082 LO 6
[0018,1020] SoftwareVersions TEST LO 4
[0018,1181] CollimatorType NONE CS 4
[0018,1200] DateOfLastCalibration [2] 20210512, 20210414 DA 18
[0018,1201] TimeOfLastCalibration [2] 063000.000000, 120434.000000 TM 28
[0018,1210] ConvolutionKernel XYZ Gauss2.00 SH 14
[0018,1242] ActualFrameDuration 1200000 IS 8
[0018,1250] ReceiveCoilName Test SH 4
[0018,5100] PatientPosition HFS CS 4
[0020,000d] StudyInstanceUID 1.3.51.0.1.1.140.140.21.70.2684395.2684374 UI 42
[0020,000e] SeriesInstanceUID 1.3.12.2.1107.5.1.4.31082.30000021051207560011000006757 UI 56
[0020,0010] StudyID 00000 SH 6
[0020,0011] SeriesNumber 10 IS 2
[0020,0012] AcquisitionNumber 2001 IS 4
[0020,0013] InstanceNumber 1 IS 2
[0020,0032] ImagePositionPatient [3] -202.237, -400.857, -394.5 DS 24
[0020,0037] ImageOrientationPatient [6] 1, 0, 0, 0, 1, 0 DS 12
[0020,0052] FrameOfReferenceUID 1.3.12.2.1107.5.1.4.31082.30000021051207031816500000026 UI 56
[0020,1040] PositionReferenceIndicator LO 0
[0020,1041] SliceLocation -394.5 DS 6
[0020,4000] ImageComments Frame 1 of 1^AC CT Brain 3.0 J30f LT 36
[0028,0002] SamplesPerPixel 1 US 2
[0028,0004] PhotometricInterpretation MONOCHROME2 CS 12
[0028,0010] Rows 400 US 2
[0028,0011] Columns 400 US 2
[0028,0030] PixelSpacing [2] 1.01821, 1.01821 DS 16
[0028,0051] CorrectedImage [6] NORM, DTIM, ATTN, SCAT, DECY, RAN CS 28
[0028,0100] BitsAllocated 16 US 2
[0028,0101] BitsStored 16 US 2
[0028,0102] HighBit 15 US 2
[0028,0103] PixelRepresentation 0 US 2
[0028,0106] SmallestImagePixelValue 0 US 2
[0028,0107] LargestImagePixelValue 65535 US 2
[0028,1050] WindowCenter 224 DS 4
[0028,1051] WindowWidth 448 DS 4
[0028,1052] RescaleIntercept 0 DS 2
[0028,1053] RescaleSlope 0.00684244 DS 10
[0028,1054] RescaleType BQML LO 4
[0032,000a] RETIRED_StudyStatusID COMPLETED CS 10
[0032,000c] RETIRED_StudyPriorityID NORMAL CS 6
[0032,1030] RETIRED_ReasonForStudy "" LO 2
[0032,1032] RequestingPhysician PN 0
[0032,1033] RequestingService LO 0
[0032,1060] RequestedProcedureDescription "" LO 2
[0032,4000] RETIRED_StudyComments "" LT 2
[0038,0300] CurrentPatientLocation Home LO 4
[0040,0009] ScheduledProcedureStepID " " SH 12
[0040,0253] PerformedProcedureStepID "" SH 2
[0040,0254] PerformedProcedureStepDescription "" LO 2
[0040,1001] RequestedProcedureID " " SH 12
[0054,0013] EnergyWindowRangeSequence SQ 40
[fffe,e000] Item na 24
[0054,0014] EnergyWindowLowerLimit 435 DS 4
[0054,0015] EnergyWindowUpperLimit 650 DS 4
[0054,0016] RadiopharmaceuticalInformationSequence SQ 420
[fffe,e000] Item na 404
[0018,0031] Radiopharmaceutical Fluorethyltyrosin LO 18
[0018,1072] RadiopharmaceuticalStartTime 131001.000000 TM 14
[0018,1074] RadionuclideTotalDose 206000000 DS 10
[0018,1075] RadionuclideHalfLife 6586.2 DS 6
[0018,1076] RadionuclidePositronFraction 0.9673 DS 6
[0018,1078] RadiopharmaceuticalStartDateTime 20210512131001.000000 DT 22
[0054,0300] RadionuclideCodeSequence SQ 118
[fffe,e000] Item na 102
[0008,0100] CodeValue C-111A1 SH 8
[0008,0102] CodingSchemeDesignator SRT SH 4
[0008,0104] CodeMeaning ^18^Fluorine LO 12
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20070625000000.000000 DT 22
[0008,010f] ContextIdentifier 4020 CS 4
[0054,0304] RadiopharmaceuticalCodeSequence SQ 130
[fffe,e000] Item na 114
[0008,0100] CodeValue C-B07E0 SH 8
[0008,0102] CodingSchemeDesignator SRT SH 4
[0008,0104] CodeMeaning Fluorethyltyrosin F^18^ LO 24
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20070625000000.000000 DT 22
[0008,010f] ContextIdentifier 4021 CS 4
[0054,0081] NumberOfSlices 74 US 2
[0054,0101] NumberOfTimeSlices 1 US 2
[0054,0410] PatientOrientationCodeSequence SQ 244
[fffe,e000] Item na 228
[0008,0100] CodeValue F-10450 SH 8
[0008,0102] CodingSchemeDesignator 99SDM SH 6
[0008,0104] CodeMeaning recumbent LO 10
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20020904000000.000000 DT 22
[0008,010f] ContextIdentifier 19 CS 2
[0054,0412] PatientOrientationModifierCodeSequence SQ 112
[fffe,e000] Item na 96
[0008,0100] CodeValue F-10340 SH 8
[0008,0102] CodingSchemeDesignator 99SDM SH 6
[0008,0104] CodeMeaning supine LO 6
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20020904000000.000000 DT 22
[0008,010f] ContextIdentifier 20 CS 2
[0054,0414] PatientGantryRelationshipCodeSequence SQ 116
[fffe,e000] Item na 100
[0008,0100] CodeValue F-10470 SH 8
[0008,0102] CodingSchemeDesignator 99SDM SH 6
[0008,0104] CodeMeaning headfirst LO 10
[0008,0105] MappingResource DCMR CS 4
[0008,0106] ContextGroupVersion 20020904000000.000000 DT 22
[0008,010f] ContextIdentifier 21 CS 2
[0054,1000] SeriesType [2] DYNAMIC, IMAGE CS 14
[0054,1001] Units BQML CS 4
[0054,1002] CountsSource EMISSION CS 8
[0054,1100] RandomsCorrectionMethod DLYD CS 4
[0054,1101] AttenuationCorrectionMethod measured,AC CT Brain 3.0 J30f LO 32
[0054,1102] DecayCorrection START CS 6
[0054,1103] ReconstructionMethod PSF+TOF 5i21s LO 14
[0054,1105] ScatterCorrectionMethod Model-based, relative scatter scaling LO 38
[0054,1200] AxialAcceptance 49 DS 2
[0054,1201] AxialMash [2] 5, 6 IS 4
[0054,1300] FrameReferenceTime 1793686.2979257 DS 16
[0054,1321] DecayFactor 1.20777 DS 8
[0054,1322] DoseCalibrationFactor 33010000 DS 8
[0054,1323] ScatterFractionFactor 0.257761 DS 8
[0054,1330] ImageIndex 1 US 2
[7fe0,0010] PixelData 0000 OW 320000