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  2. XNAT ROI Plugin
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Unable to export Mask-based ROI

Issue #42 open
Tom Roberts created an issue

I have X-Ray DICOM data. I want to draw a mask on the images using the OHIF XNAT Viewer. I can successfully use the Mask tool to segment a region, however, when I press on the Export button in the Mask-based ROIs menu, it doesn’t work and produces the following Error message:

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DICOM dump here (same as related Issue with Contour tool):

Dicom-File-Format

Dicom-Meta-Information-Header

Used TransferSyntax: Little Endian Explicit

(0002,0000) UL 182 # 4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion
(0002,0002) UI =ComputedRadiographyImageStorage # 26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.3.12.2.1107.5.4.4.1385.30000010110508145200000000048] # 54, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianExplicit # 20, 1 TransferSyntaxUID
(0002,0012) UI [1.2.40.0.13.1.1] # 16, 1 ImplementationClassUID
(0002,0013) SH [dcm4che-2.0] # 12, 1 ImplementationVersionName

Dicom-Data-Set

Used TransferSyntax: Little Endian Explicit

(0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet
(0008,0008) CS [DERIVED\SECONDARY\CSA RESAMPLED] # 32, 4 ImageType
(0008,0016) UI =ComputedRadiographyImageStorage # 26, 1 SOPClassUID
(0008,0018) UI [1.3.12.2.1107.5.4.4.1385.30000010110508145200000000048] # 54, 1 SOPInstanceUID
(0008,0020) DA [20101114] # 8, 1 StudyDate
(0008,0021) DA [20101114] # 8, 1 SeriesDate
(0008,0022) DA [20101114] # 8, 1 AcquisitionDate
(0008,0023) DA [20101114] # 8, 1 ContentDate
(0008,0030) TM (no value available) # 0, 0 StudyTime
(0008,0033) TM (no value available) # 0, 0 ContentTime
(0008,0050) SH [1542-1542_SCHXR_1_M_W_47] # 24, 1 AccessionNumber
(0008,0060) CS [CR] # 2, 1 Modality
(0008,0070) LO [SIEMENS] # 8, 1 Manufacturer
(0008,0090) PN (no value available) # 0, 0 ReferringPhysicianName
(0008,1030) LO [XR Scaphoid Rt] # 14, 1 StudyDescription
(0008,1032) SQ (Sequence with undefined length #=1) # u/l, 1 ProcedureCodeSequence
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0008,0100) SH [XSCAR] # 6, 1 CodeValue
(0008,0102) SH [SECTRA] # 6, 1 CodingSchemeDesignator
(0008,0104) LO [XR Scaphoid Rt] # 14, 1 CodeMeaning
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0008,103e) LO [X Scaphoid DP] # 14, 1 SeriesDescription
(0008,1090) LO [SIEMENS FD-X] # 12, 1 ManufacturerModelName
(0010,0010) PN [1542] # 4, 1 PatientName
(0010,0020) LO [1542] # 4, 1 PatientID
(0010,0030) DA (no value available) # 0, 0 PatientBirthDate
(0010,0040) CS [M] # 2, 1 PatientSex
(0010,1010) AS [047Y] # 4, 1 PatientAge
(0010,1030) DS [0] # 2, 1 PatientWeight
(0012,0064) SQ (Sequence with undefined length #=1) # u/l, 1 DeidentificationMethodCodeSequence
(fffe,e000) na (Item with undefined length #=4) # u/l, 1 Item
(0008,0100) SH [289354] # 6, 1 CodeValue
(0008,0102) SH [XNAT] # 4, 1 CodingSchemeDesignator
(0008,0103) SH [1.0] # 4, 1 CodingSchemeVersion
(0008,0104) LO [XNAT DicomEdit 6 Script] # 24, 1 CodeMeaning
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0018,0010) LO (no value available) # 0, 0 ContrastBolusAgent
(0018,0015) CS [WRIST] # 6, 1 BodyPartExamined
(0018,0060) DS [60] # 2, 1 KVP
(0018,1020) LO [VB21B] # 6, 1 SoftwareVersions
(0018,1110) DS [934] # 4, 1 DistanceSourceToDetector
(0018,1150) IS [5] # 2, 1 ExposureTime
(0018,1151) IS [394] # 4, 1 XRayTubeCurrent
(0018,1152) IS [2] # 2, 1 Exposure
(0018,1153) IS [2210] # 4, 1 ExposureInuAs
(0018,115e) DS [0.06] # 4, 1 ImageAndFluoroscopyAreaDoseProduct
(0018,1160) SH [NONE] # 4, 1 FilterType
(0018,1164) DS [0.143\0.143] # 12, 2 ImagerPixelSpacing
(0018,1166) CS [NONE] # 4, 1 Grid
(0018,1180) SH [----] # 4, 1 CollimatorGridName
(0018,1401) LO [0] # 2, 1 AcquisitionDeviceProcessingCode
(0018,1405) IS [1455] # 4, 1 RelativeXRayExposure
(0018,5100) CS (no value available) # 0, 0 PatientPosition
(0018,5101) CS (no value available) # 0, 0 ViewPosition
(0018,6000) DS [400] # 4, 1 Sensitivity
(0018,7000) CS [YES] # 4, 1 DetectorConditionsNominalFlag
(0018,7001) DS [42] # 2, 1 DetectorTemperature
(0020,000d) UI [1.2.840.113619.2.243.339070193158.40485.4839.225393] # 52, 1 StudyInstanceUID
(0020,000e) UI [1.3.12.2.1107.5.4.4.1385.30000010110508281131200000047] # 54, 1 SeriesInstanceUID
(0020,0010) SH [1542_SCHXR_1_M_W_471542] # 24, 1 StudyID
(0020,0011) IS [1] # 2, 1 SeriesNumber
(0020,0012) IS [1] # 2, 1 AcquisitionNumber
(0020,0013) IS [1] # 2, 1 InstanceNumber
(0020,0020) CS (no value available) # 0, 0 PatientOrientation
(0020,0060) CS (no value available) # 0, 0 Laterality
(0028,0002) US 1 # 2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation
(0028,0010) US 964 # 2, 1 Rows
(0028,0011) US 964 # 2, 1 Columns
(0028,0100) US 16 # 2, 1 BitsAllocated
(0028,0101) US 12 # 2, 1 BitsStored
(0028,0102) US 11 # 2, 1 HighBit
(0028,0103) US 0 # 2, 1 PixelRepresentation
(0028,0301) CS [NO] # 2, 1 BurnedInAnnotation
(0028,1050) DS [1299] # 4, 1 WindowCenter
(0028,1051) DS [1220] # 4, 1 WindowWidth
(0028,2110) CS [00] # 2, 1 LossyImageCompression
(0032,1064) SQ (Sequence with undefined length #=1) # u/l, 1 RequestedProcedureCodeSequence
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0008,0100) SH [XSCAR] # 6, 1 CodeValue
(0008,0102) SH [BROKER] # 6, 1 CodingSchemeDesignator
(0008,0104) LO [XR Scaphoid Rt] # 14, 1 CodeMeaning
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0040,0260) SQ (Sequence with undefined length #=1) # u/l, 1 PerformedProtocolCodeSequence
(fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
(0008,0100) SH [XSCAR] # 6, 1 CodeValue
(0008,0102) SH [BROKER] # 6, 1 CodingSchemeDesignator
(0008,0104) LO [XR Scaphoid Rt] # 14, 1 CodeMeaning
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0040,2016) LO (no value available) # 0, 0 PlacerOrderNumberImagingServiceRequest
(0040,2017) LO (no value available) # 0, 0 FillerOrderNumberImagingServiceRequest
(0040,a073) SQ (Sequence with explicit length #=0) # 0, 1 VerifyingObserverSequence
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
(0040,a075) PN (no value available) # 0, 0 VerifyingObserverName
(0040,a088) SQ (Sequence with explicit length #=0) # 0, 1 VerifyingObserverIdentificationCodeSequence
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
(0040,a123) PN (no value available) # 0, 0 PersonName
(0070,0001) SQ (Sequence with explicit length #=0) # 0, 1 GraphicAnnotationSequence
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
(0070,0084) PN (no value available) # 0, 0 ContentCreatorName
(2050,0020) CS [IDENTITY] # 8, 1 PresentationLUTShape
(7fe0,0010) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 1858592, 1 PixelData

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Thanks in advance!

Comments (3)

  2. Mo Alsad

    Hi Tom,

    Unlike the RT Structure Set Storage, the Segmentation Storage supports storing mask data for reference images without Frame of Reference UID, Plane Position (Patient) and Plane Orientation (Patient). Please refer to Section A.51.5 of the standard. The issue is that the underlying package we use to create DICOM SEG does not fully implement that part of the standard which consequently renders the error message.

    It is on our agenda to look into this issue and fix it, but in the mean time, I would not be able to give an ETA for the fix.

    Kind regards,

    Mo

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