Dicom tag not recognized

[leochan2009]

No description provided.

[leochan2009]

[fedorov]

@leochan2009 you should update Slicer. I don't know the root of this issue, but a related problem in Slicer DICOM module was fixed recently.

Related issues:

• Fixed local variable 'sec' referenced before assignment error fedorov/MultiVolumeImporter#23
• BUG: consistent return for value of uninitialized data commontk/CTK#750

[leochan2009]

@fedorov ,
thanks, Andriy, i will take a look.

[che85]

@fedorov I just checked that issue and noticed that one of the slices is corrupted:

dciodvfy output

(0x0051,0x100b) SH Acquisition Matrix Text  - Warning - Explicit value representation doesn't match data dictionary; Explicit <LO> Dictionary <SH>
Error - Seek failed - while reading unencapsulated Pixel Data
Error - Dicom dataset read failed
Warning - Unrecognized defined term <CCG_CSTemp> for value 1 of attribute <Coding Scheme Designator>
Error - Missing attribute Type 2C Conditional Element=<Laterality> Module=<GeneralSeries>
Warning - Unrecognized defined term <CCG_CSTemp> for value 1 of attribute <Coding Scheme Designator>
Error - Missing attribute Type 1C Conditional Element=<PixelData> Module=<ImagePixelMacro>
Warning - Unrecognized defined term <M> for value 3 of attribute <Image Type>
Warning - Unrecognized defined term <SAT1> for value 1 of attribute <Scan Options>
Warning - Attribute is not present in standard DICOM IOD - (0x0010,0x21c0) US Pregnancy Status 
Warning - Attribute is not present in standard DICOM IOD - (0x0032,0x1032) PN Requesting Physician 
Warning - Attribute is not present in standard DICOM IOD - (0x0032,0x1033) LO Requesting Service 
Warning - Attribute is not present in standard DICOM IOD - (0x0032,0x1060) LO Requested Procedure Description 
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x0100) SH Code Value 
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x0102) SH Coding Scheme Designator 
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x0104) LO Code Meaning 
Warning - Attribute is not present in standard DICOM IOD - (0x0032,0x1064) SQ Requested Procedure Code Sequence 
Warning - Dicom dataset contains attributes not present in standard DICOM IOD - this is a Standard Extended SOP Class

How should we handle such situations?

  def createLoadableFileListForSeries(self, series):
    seriesNumber = RegistrationResult.getSeriesNumberFromString(series)
    loadableList = []
    for dcm in self.getFileList(self.intraopDICOMDirectory):
      currentFile = os.path.join(self.intraopDICOMDirectory, dcm)
      # at the following line it crashes
      currentSeriesNumber = int(self.getDICOMValue(currentFile, DICOMTAGS.SERIES_NUMBER))
      if currentSeriesNumber and currentSeriesNumber == seriesNumber:
        loadableList.append(currentFile)
    return loadableList

[fedorov]

Error - Missing attribute Type 1C Conditional Element=<PixelData>

This seems to be a fatal situation, and the action is very straightforward - if the input series does not have PixelData, there is really nothing we can do with it.

[fedorov]

The real question is how could this kind of data could be produced by the scanner if the standard acquisition protocol was followed. Something must be different about that case.

[che85]

It’s one corrupt file in case 592 intraop images. File names and extension also differs from the usual intraop protocol...

[fedorov]

It must have a different Series/StudyInstanceUID from any other instances, right?

If that is the case, it means we also need to add another check to ignore any of the instances that have inconsistent StudyInstanceUID.