kmader/0-Overview.md

## 0-Overview.md

      
    Raw
  

              0-Overview.md
            
          
    Loading Issue

I think the image loading problem is related to the 'Load group files' checkbox, if you leave it unchecked it seems to work fine.
The error message is:
ERROR Image Reader         3:38       Execute failed: Encountered duplicate row ID  "/Users/mader/Documents/TCGA_DICOMS/DOI/TCGA-17-Z011/1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452/1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284/000000.dcm" at row number 3

The test file is attached as 000000.dcm
Metadata Issue

If you tell it to read the metadata in a separate column you get a very simple metadata (even if you check read none ome-xml metadata) (knime META data) and reading it in FIJI (or any other standard DICOM tool) gives you much more information

  
## 000000.dcm

      
    Raw
  

              000000.dcm
            
          
            View raw
        
    
## 1-KNIME-Metadata.xml
<?xml version='1.0' encoding='UTF-8'?>

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">

    <Image ID="Image:0" Name="/Users/mader/Documents/TCGA_DICOMS/DOI/TCGA-17-Z011/1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452/1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284/000000.dcm">

        <Description>ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI</Description>

        <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SizeC="1" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" TimeIncrement="1.0" TimeIncrementUnit="s" Type="uint16">

            <Channel ID="Channel:0:0" SamplesPerPixel="1">

                <LightPath>

                </LightPath>

            </Channel>

        </Pixels>

    </Image>

</OME>

## 2-FIJI_ShowInfo.txt
0002,0002  Media Storage SOP Class UID: 1.2.840.10008.5.1.4.1.1.2
0002,0003  Media Storage SOP Inst UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.980866767382610241733918262437
0002,0010  Transfer Syntax UID: 1.2.840.10008.1.2
0002,0012  Implementation Class UID: 1.2.40.0.13.1.1.1
0002,0013  Implementation Version Name: dcm4che-1.4.31
0008,0000  ---: �
0008,0005  Specific Character Set: ISO_IR 100
0008,0008  Image Type: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
0008,0016  SOP Class UID: 1.2.840.10008.5.1.4.1.1.2
0008,0018  SOP Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.980866767382610241733918262437
0008,0020  Study Date: 19820905
0008,0021  Series Date: 19820905
0008,0022  Acquisition Date: 19820905
0008,0023  Image Date: 19820905
0008,0030  Study Time: 134213.343000
0008,0031  Series Time: 134810.468000
0008,0032  Acquisition Time: 134702.346000
0008,0033  Image Time: 134702.346000
0008,0040  Data Set Type: 0
0008,0041  Data Set Subtype: IMA SPI
0008,0050  Accession Number: 1812620217297656
0008,0060  Modality: CT
0008,0070  Manufacturer: SIEMENS
0008,0090  Referring Physician's Name:
0008,1010  Station Name:
0008,103E  Series Description: Chest Routine #2
0008,1080  Admitting Diagnoses Description:
0008,1090  Manufacturer's Model Name: Volume Zoom
0008,2111  Derivation Description:
0009,0000  ---: N
0009,0010  ---: SIEMENS CT VA1 DUMMY
0009,0011  ---: SPI RELEASE 1
0009,0012  ---: SIEMENS CM VA0  CMS
0010,0000  ---: N
0010,0010  Patient's Name: TCGA-17-Z011
0010,0020  Patient ID: TCGA-17-Z011
0010,0030  Patient's Birth Date:
0010,0040  Patient's Sex: M
0010,1010  Patient's Age: 069Y
0010,4000  Patient Comments:
0011,0000  ---: *
0011,0010  ---: SPI RELEASE 1
0011,0011  ---: SIEMENS ISI
0012,0000  ---: �
0012,0062  ---: YES
0013,0000  ---: .
0013,0010  ---: CTP
0013,1010  ---: TCGA-LUAD
0013,1013  ---: 77779002
0018,0000  ---: �
0018,0015  Body Part Examined: CHEST
0018,0050  Slice Thickness: 5
0018,0060  kVp: 140
0018,1020  Software Versions(s): VA11Bs
0018,1030  Protocol Name: Chest Routine
0018,1100  Reconstruction Diameter: 334
0018,1110  Distance Source to Detector: 1040
0018,1111  Distance Source to Patient: 570
0018,1120  Gantry/Detector Tilt: 0
0018,1130  Table Height: 162
0018,1140  Rotation Direction: CW
0018,1150  Exposure Time: 500
0018,1151  X-ray Tube Current: 391
0018,1152  Exposure: 120
0018,1160  Filter Type: 0
0018,1170  Generator Power: 54
0018,1190  Focal Spot(s): 1.2
0018,1210  Convolution Kernel: B60f
0018,5100  Patient Position: HFS
0019,0000  ---: l
0019,0010  ---: SIEMENS CT VA0  COAD
0019,0011  ---: SIEMENS CM VA0  CMS
0019,1090  ---: 0
0019,1092  ---: 1
0019,1093  ---: 0
0019,1096  ---: 0
0019,10B0  ---: 16.3
0020,0000  ---: ~
0020,000D  Study Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452
0020,000E  Series Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284
0020,0010  Study ID:
0020,0011  Series Number: 3
0020,0012  Acquisition Number: 2
0020,0013  Image Number: 1
0020,0030  Image Position: -167\-167\0
0020,0032  Image Position (Patient): -166\-329\-31
0020,0035  ---: 1\0\0\0\1\0
0020,0037  Image Orientation (Patient): 1\0\0\0\1\0
0020,0050  Location: -31
0020,0052  Frame of Reference UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.377837516050283598442451217275
0020,0070  Image Geometry Type: PLANAR
0020,1040  Position Reference Indicator:
0020,1041  Slice Location: -31
0021,0000  ---:
0021,0010  ---: SIEMENS MED
0028,0000  ---:
0028,0002  Samples per Pixel: 1
0028,0004  Photometric Interpretation: MONOCHROME2
0028,0005  ---:
0028,0008  Number of Frames: 1
0028,0010  Rows: 512
0028,0011  Columns: 512
0028,0030  Pixel Spacing: 006.523438e-01\006.523438e-01
0028,0040  ---: RECT
0028,0060  ---: NONE
0028,0100  Bits Allocated: 16
0028,0101  Bits Stored: 12
0028,0102  High Bit: 11
0028,0103  Pixel Representation: 0
0028,0200  ---: �
0028,0301  Burned In Annotation: NO
0028,0303  ---: MODIFIED
0028,1050  Window Center: 30
0028,1051  Window Width: 400
0028,1052  Rescale Intercept: -1024
0028,1053  Rescale Slope: 1
0028,1055  Window Center & Width Explanation: WINDOW1\WINDOW2
0029,0000  ---: T
0029,0010  ---: SIEMENS CSA HEADER
0029,0011  ---: SIEMENS MEDCOM HEADER
0029,0012  ---: SIEMENS MED DISPLAY
0032,0000  ---: X
0032,000A  Study Status ID: SCHEDULED
0032,1000  Scheduled Study Start Date: 19820905
0032,1001  Scheduled Study Start Time: 130000.000000
0032,1060  Requested Procedure Description: CT CHEST W CONT
0032,4000  Study Comments:
0040,0000  ---:
0040,1003  Requested Procedure Priority:
0091,0000  ---:
0091,0010  ---: SIENET
0095,0000  ---:
0095,0010  ---: SIENET
0097,0000  ---:
0097,0010  ---: SIENET
0099,0000  ---:
0099,0010  ---: SIENET
7003,0000  ---:
7003,0010  ---: SIEMENS MED
7FE0,0010  Pixel Data: 3334
	<?xml version='1.0' encoding='UTF-8'?>

	<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">

	<Image ID="Image:0" Name="/Users/mader/Documents/TCGA_DICOMS/DOI/TCGA-17-Z011/1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452/1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284/000000.dcm">

	<Description>ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI</Description>

	<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" PhysicalSizeX="1.0" PhysicalSizeXUnit="µm" PhysicalSizeY="1.0" PhysicalSizeYUnit="µm" PhysicalSizeZ="1.0" PhysicalSizeZUnit="µm" SizeC="1" SizeT="1" SizeX="512" SizeY="512" SizeZ="1" TimeIncrement="1.0" TimeIncrementUnit="s" Type="uint16">

	<Channel ID="Channel:0:0" SamplesPerPixel="1">

	<LightPath>

	</LightPath>

	</Channel>

	</Pixels>

	</Image>

	</OME>
	0002,0002 Media Storage SOP Class UID: 1.2.840.10008.5.1.4.1.1.2
	0002,0003 Media Storage SOP Inst UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.980866767382610241733918262437
	0002,0010 Transfer Syntax UID: 1.2.840.10008.1.2
	0002,0012 Implementation Class UID: 1.2.40.0.13.1.1.1
	0002,0013 Implementation Version Name: dcm4che-1.4.31
	0008,0000 ---: �
	0008,0005 Specific Character Set: ISO_IR 100
	0008,0008 Image Type: ORIGINAL\PRIMARY\AXIAL\CT_SOM5 SPI
	0008,0016 SOP Class UID: 1.2.840.10008.5.1.4.1.1.2
	0008,0018 SOP Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.980866767382610241733918262437
	0008,0020 Study Date: 19820905
	0008,0021 Series Date: 19820905
	0008,0022 Acquisition Date: 19820905
	0008,0023 Image Date: 19820905
	0008,0030 Study Time: 134213.343000
	0008,0031 Series Time: 134810.468000
	0008,0032 Acquisition Time: 134702.346000
	0008,0033 Image Time: 134702.346000
	0008,0040 Data Set Type: 0
	0008,0041 Data Set Subtype: IMA SPI
	0008,0050 Accession Number: 1812620217297656
	0008,0060 Modality: CT
	0008,0070 Manufacturer: SIEMENS
	0008,0090 Referring Physician's Name:
	0008,1010 Station Name:
	0008,103E Series Description: Chest Routine #2
	0008,1080 Admitting Diagnoses Description:
	0008,1090 Manufacturer's Model Name: Volume Zoom
	0008,2111 Derivation Description:
	0009,0000 ---: N
	0009,0010 ---: SIEMENS CT VA1 DUMMY
	0009,0011 ---: SPI RELEASE 1
	0009,0012 ---: SIEMENS CM VA0 CMS
	0010,0000 ---: N
	0010,0010 Patient's Name: TCGA-17-Z011
	0010,0020 Patient ID: TCGA-17-Z011
	0010,0030 Patient's Birth Date:
	0010,0040 Patient's Sex: M
	0010,1010 Patient's Age: 069Y
	0010,4000 Patient Comments:
	0011,0000 ---: *
	0011,0010 ---: SPI RELEASE 1
	0011,0011 ---: SIEMENS ISI
	0012,0000 ---: �
	0012,0062 ---: YES
	0013,0000 ---: .
	0013,0010 ---: CTP
	0013,1010 ---: TCGA-LUAD
	0013,1013 ---: 77779002
	0018,0000 ---: �
	0018,0015 Body Part Examined: CHEST
	0018,0050 Slice Thickness: 5
	0018,0060 kVp: 140
	0018,1020 Software Versions(s): VA11Bs
	0018,1030 Protocol Name: Chest Routine
	0018,1100 Reconstruction Diameter: 334
	0018,1110 Distance Source to Detector: 1040
	0018,1111 Distance Source to Patient: 570
	0018,1120 Gantry/Detector Tilt: 0
	0018,1130 Table Height: 162
	0018,1140 Rotation Direction: CW
	0018,1150 Exposure Time: 500
	0018,1151 X-ray Tube Current: 391
	0018,1152 Exposure: 120
	0018,1160 Filter Type: 0
	0018,1170 Generator Power: 54
	0018,1190 Focal Spot(s): 1.2
	0018,1210 Convolution Kernel: B60f
	0018,5100 Patient Position: HFS
	0019,0000 ---: l
	0019,0010 ---: SIEMENS CT VA0 COAD
	0019,0011 ---: SIEMENS CM VA0 CMS
	0019,1090 ---: 0
	0019,1092 ---: 1
	0019,1093 ---: 0
	0019,1096 ---: 0
	0019,10B0 ---: 16.3
	0020,0000 ---: ~
	0020,000D Study Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452
	0020,000E Series Instance UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284
	0020,0010 Study ID:
	0020,0011 Series Number: 3
	0020,0012 Acquisition Number: 2
	0020,0013 Image Number: 1
	0020,0030 Image Position: -167\-167\0
	0020,0032 Image Position (Patient): -166\-329\-31
	0020,0035 ---: 1\0\0\0\1\0
	0020,0037 Image Orientation (Patient): 1\0\0\0\1\0
	0020,0050 Location: -31
	0020,0052 Frame of Reference UID: 1.3.6.1.4.1.14519.5.2.1.7777.9002.377837516050283598442451217275
	0020,0070 Image Geometry Type: PLANAR
	0020,1040 Position Reference Indicator:
	0020,1041 Slice Location: -31
	0021,0000 ---:
	0021,0010 ---: SIEMENS MED
	0028,0000 ---:
	0028,0002 Samples per Pixel: 1
	0028,0004 Photometric Interpretation: MONOCHROME2
	0028,0005 ---:
	0028,0008 Number of Frames: 1
	0028,0010 Rows: 512
	0028,0011 Columns: 512
	0028,0030 Pixel Spacing: 006.523438e-01\006.523438e-01
	0028,0040 ---: RECT
	0028,0060 ---: NONE
	0028,0100 Bits Allocated: 16
	0028,0101 Bits Stored: 12
	0028,0102 High Bit: 11
	0028,0103 Pixel Representation: 0
	0028,0200 ---: �
	0028,0301 Burned In Annotation: NO
	0028,0303 ---: MODIFIED
	0028,1050 Window Center: 30
	0028,1051 Window Width: 400
	0028,1052 Rescale Intercept: -1024
	0028,1053 Rescale Slope: 1
	0028,1055 Window Center & Width Explanation: WINDOW1\WINDOW2
	0029,0000 ---: T
	0029,0010 ---: SIEMENS CSA HEADER
	0029,0011 ---: SIEMENS MEDCOM HEADER
	0029,0012 ---: SIEMENS MED DISPLAY
	0032,0000 ---: X
	0032,000A Study Status ID: SCHEDULED
	0032,1000 Scheduled Study Start Date: 19820905
	0032,1001 Scheduled Study Start Time: 130000.000000
	0032,1060 Requested Procedure Description: CT CHEST W CONT
	0032,4000 Study Comments:
	0040,0000 ---:
	0040,1003 Requested Procedure Priority:
	0091,0000 ---:
	0091,0010 ---: SIENET
	0095,0000 ---:
	0095,0010 ---: SIENET
	0097,0000 ---:
	0097,0010 ---: SIENET
	0099,0000 ---:
	0099,0010 ---: SIENET
	7003,0000 ---:
	7003,0010 ---: SIEMENS MED
	7FE0,0010 Pixel Data: 3334