Unable to load image cone beam CT from Carestream
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Roberto Fichera
May 14, 2018, 5:42:16 AM5/14/18
to Orthanc Users
Hi Guys,
I've just got this problem when trying to upload Cone Beam images from a Carestream device, below the log.
Please let me know what I can do to get Orthanc v1.3.2 to accept such images.
Thanks in advance,
Roberto Fichera.
May 14 09:10:56 localhost Orthanc[649]: W: Found element (0009,11a0) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Length of element (0009,11a1) is odd
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Dataset not in ascending tag order, at element (0000,0000)
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Element (0000,0000) found twice in one data set or item, ignoring second entry
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Element (0000,0000) found twice in one data set or item, ignoring second entry
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Element (0000,0000) found twice in one data set or item, ignoring second entry
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Element (0000,0000) found twice in one data set or item, ignoring second entry
May 14 09:10:56 localhost Orthanc[649]: W: DcmItem: Length of element (028f,028b) is odd
May 14 09:11:04 localhost Orthanc[649]: E: DcmElement: Unknown Tag & Data (028f,028b) larger (39846519) than remaining bytes (563228) in file, premature end of stream
May 14 09:11:04 localhost Orthanc[649]: W: DIMSE Warning: (KPServer,ORTHANC): DIMSE receiveDataSetInMemory: dset->read() Failed (Invalid stream)
May 14 09:11:04 localhost Orthanc[649]: E0514 09:11:04.644651 StoreScp.cpp:294] Store SCP Failed: DIMSE Failed to receive message
and below you can see the tags details show by python pydicom library
In [1]: from pydicom import dicomio
In [2]: i = dicomio.read_file('export.dcm')
In [3]: i
Out[3]:
(0008, 0005) Specific Character Set CS: 'ISO_IR 192'
(0008, 0008) Image Type CS: ['DERIVED', 'PRIMARY', 'VOLUME', 'RESAMPLED']
(0008, 0012) Instance Creation Date DA: '20180514'
(0008, 0013) Instance Creation Time TM: '111411'
(0008, 0016) SOP Class UID UI: X-Ray 3D Craniofacial Image Storage
(0008, 0018) SOP Instance UID UI: 1.2.250.1.90.2.772081700.20180514111411.5796.12204
(0008, 0020) Study Date DA: '20180406'
(0008, 0021) Series Date DA: '20180514'
(0008, 0022) Acquisition Date DA: '20180406'
(0008, 0023) Content Date DA: '20180514'
(0008, 0030) Study Time TM: '180549'
(0008, 0031) Series Time TM: '111411'
(0008, 0032) Acquisition Time TM: '180741'
(0008, 0033) Content Time TM: '111411'
(0008, 0050) Accession Number SH: ''
(0008, 0060) Modality CS: 'DX'
(0008, 0070) Manufacturer LO: 'Carestream Health'
(0008, 0080) Institution Name LO: 'XXXXXXX'
(0008, 0090) Referring Physician's Name PN: 'XXXXXXX'
(0008, 1030) Study Description LO: ''
(0008, 103e) Series Description LO: 'Exported Volume'
(0008, 1040) Institutional Department Name LO: 'RADIOLOGY'
(0008, 1090) Manufacturer's Model Name LO: 'CS 9000'
(0008, 9206) Volumetric Properties CS: 'VOLUME'
(0008, 9207) Volume Based Calculation Technique CS: 'MPR'
(0009, 0011) Private Creator LO: 'TROPHY'
(0009, 11a0) Private tag data 4 item(s) ----
(0009, 11a1) Private tag data LO: '3DACQ_FUNCTION_MODE'
(0009, 11a2) Private tag data UL: 6
(0009, 11a3) Private tag data UN: 'Normal'
---------
(0009, 11a1) Private tag data LO: '3DACQ_NB_VOLUME_TO_STITCH'
(0009, 11a2) Private tag data UL: 1
(0009, 11a3) Private tag data UN: '1\x00'
---------
(0009, 11a1) Private tag data LO: '3DACQ_SCAN_MODE'
(0009, 11a2) Private tag data UL: 8
(0009, 11a3) Private tag data UN: 'FullScan'
---------
(0009, 11a1) Private tag data LO: '3DACQ_SCAN_OBJECT'
(0009, 11a2) Private tag data UL: 7
(0009, 11a3) Private tag data UN: 'Patient\x00'
---------
(0010, 0010) Patient's Name PN: 'XXXXX^YYYYY'
(0010, 0020) Patient ID LO: '7884839267658269838482696577926866926546828671926548484848494856'
(0010, 0030) Patient's Birth Date DA: 'XXXXMMDD'
(0010, 0040) Patient's Sex CS: 'O'
(0018, 0015) Body Part Examined CS: 'JAW'
(0018, 1000) Device Serial Number LO: 'BEBH009'
(0018, 1020) Software Version(s) LO: ['AcqPanoramic.dll##5.4.4.32##01/07/14', 'Pano.dll##5.4.4.32##01/07/14', 'Odt2000.dll##5.4.4.32##01/07/14', 'TPjbus.dll##5.4.4.32##01/07/14', 'Trajectory.dll##5.4.4.32##01/07/14', 'TPita.dll##5.4.4.32##01/07/14', 'TaskVolumizer.dll##3.1.12.0##22/05/2014##W32', 'CS Volume Converter##1.0.9.0##29/02/12']
(0018, 9507) X-Ray 3D Acquisition Sequence 1 item(s) ----
(0018, 0060) KVP DS: "70"
(0018, 115e) Image and Fluoroscopy Area Dose Pro DS: "2.6127864"
(0018, 7004) Detector Type CS: 'SCINTILLATOR'
(0018, 700a) Detector ID SH: 'BDTD044/VBAJ11'
(0018, 702a) Detector Manufacturer Name LO: 'Carestream Health'
(0018, 702b) Detector Manufacturer's Model Name LO: '3D_V1'
(0018, 9328) Exposure Time in ms FD: 10800.0
(0018, 9330) X-Ray Tube Current in mA FD: 12.0
(0018, 9516) Start Acquisition DateTime DT: '20180406180741'
(0020, 0012) Acquisition Number IS: '1'
---------
(0018, 9530) X-Ray 3D Reconstruction Sequence 1 item(s) ----
(0018, 9524) Application Name LO: 'CS Volume Converter'
(0018, 9525) Application Version LO: '1.0.9.0'
(0018, 9526) Application Manufacturer LO: 'Carestream'
---------
(0020, 000d) Study Instance UID UI: 1.2.250.1.90.4.772081700.20180406180549.2564.16
(0020, 000e) Series Instance UID UI: 1.2.250.1.90.3.772081700.20180514111411.5796.12202
(0020, 0010) Study ID SH: '1.2.250.1.90.1.772081700.1523030489.683'
(0020, 0011) Series Number IS: '1'
(0020, 0013) Instance Number IS: '1'
(0020, 0020) Patient Orientation CS: ['L', 'P']
(0020, 0052) Frame of Reference UID UI: 1.2.250.1.90.5.772081700.20180406180813.6140.33
(0020, 1040) Position Reference Indicator LO: ''
(0020, 4000) Image Comments LT: '3D acquisition mode: Simple volume'
(0028, 0002) Samples per Pixel US: 1
(0028, 0004) Photometric Interpretation CS: 'MONOCHROME2'
(0028, 0008) Number of Frames IS: '357'
(0028, 0010) Rows US: 541
(0028, 0011) Columns US: 541
(0028, 0100) Bits Allocated US: 16
(0028, 0101) Bits Stored US: 16
(0028, 0102) High Bit US: 15
(0028, 0103) Pixel Representation US: 0
(0028, 2110) Lossy Image Compression CS: '00'
(0028, 9520) Image to Equipment Mapping Matrix DS: ['1.00000000E+000', '0.00000000E+000', '0.00000000E+000', '1.70000000E+001', '0.00000000E+000', '1.00000000E+000', '0.00000000E+000', '4.00000000E+000', '0.00000000E+000', '0.00000000E+000', '1.00000000E+000', '0.00000000E+000', '0.00000000E+000', '0.00000000E+000', '0.00000000E+000', '1.00000000E+000']
(0028, 9537) Equipment Coordinate System Identif CS: 'ISOCENTER'
(0040, 0555) Acquisition Context Sequence 0 item(s) ----
(2050, 0020) Presentation LUT Shape CS: 'IDENTITY'
(5200, 9229) Shared Functional Groups Sequence 1 item(s) ----
(0018, 9504) X-Ray 3D Frame Type Sequence 1 item(s) ----
(0008, 9007) Frame Type CS: ['DERIVED', 'PRIMARY', 'VOLUME', 'RESAMPLED']
(0008, 9206) Volumetric Properties CS: 'VOLUME'
(0008, 9207) Volume Based Calculation Technique CS: 'MPR'
(0020, 9536) Reconstruction Index US: 1
---------
(0020, 9071) Frame Anatomy Sequence 1 item(s) ----
(0008, 2218) Anatomic Region Sequence 1 item(s) ----
(0008, 0100) Code Value SH: 'T-D1213'
(0008, 0102) Coding Scheme Designator SH: 'SRT'
(0008, 0104) Code Meaning LO: 'Jaw region'
---------
(0020, 9072) Frame Laterality CS: 'U'
---------
(0020, 9113) Plane Position Sequence 0 item(s) ----
(0020, 9116) Plane Orientation Sequence 1 item(s) ----
(0020, 0037) Image Orientation (Patient) DS: ['1.00000000E+000', '0.00000000E+000', '0.00000000E+000', '0.00000000E+000', '1.00000000E+000', '0.00000000E+000']
---------
(0028, 9110) Pixel Measures Sequence 1 item(s) ----
(0018, 0050) Slice Thickness DS: "0.1"
(0028, 0030) Pixel Spacing DS: ['1.00000000E-001', '1.00000000E-001']
---------
(0028, 9132) Frame VOI LUT Sequence 1 item(s) ----
(0028, 1050) Window Center DS: "1.04800000E+003"
(0028, 1051) Window Width DS: "4.09600000E+003"
---------
(0028, 9145) Pixel Value Transformation Sequence 1 item(s) ----
(0028, 1052) Rescale Intercept DS: "-1000"
(0028, 1053) Rescale Slope DS: "1"
(0028, 1054) Rescale Type LO: 'HU'
---------
---------
(5200, 9230) Per-frame Functional Groups Sequence 357 item(s) ----
(0020, 9111) Frame Content Sequence 0 item(s) ----
(0020, 9113) Plane Position Sequence 1 item(s) ----
(0020, 0032) Image Position (Patient) DS: ['-2.70000000E+001', '-2.70000000E+001', '-1.78000000E+001']
---------
(0020, 9116) Plane Orientation Sequence 0 item(s) ----
---------
(0020, 9111) Frame Content Sequence 0 item(s) ----
(0020, 9113) Plane Position Sequence 1 item(s) ----
(0020, 0032) Image Position (Patient) DS: ['-2.70000000E+001', '-2.70000000E+001', '-1.77000000E+001']
---------
(0020, 9116) Plane Orientation Sequence 0 item(s) ----
---------
[..... other 356 blocks ....]
---------
(7fe0, 0010) Pixel Data OB: Array of 90218756 bytes
Sébastien Jodogne
May 14, 2018, 6:27:29 AM5/14/18
to Orthanc Users
Hello,
According to the Orthanc log, your DICOM file looks corrupted.
You can use the reference tool "dciodvfy" from David Clunie's dicom3tools in order to check the validity of the file wrt. the DICOM standard:
Please provide a sample (possibly anonymized) DICOM image if you want further support from the Orthanc community.
HTH,
Sébastien-
Roberto Fichera
May 14, 2018, 6:48:10 AM5/14/18
to Orthanc Users
Hi Sébastien,
I think the problem is related to not standard tags present in the image
dciodvfy /TempData/export.dcm
(0x0009,0x11a0) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a1) ? - Warning - Private tag without owner - use owner of parent sequence "TROPHY"
(0x0009,0x11a1) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a2) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a3) ? - Warning - Unrecognized tag - explicit value representation is UN
(0x0009,0x11a1) ? - Warning - Private tag without owner - use owner of parent sequence "TROPHY"
(0x0009,0x11a1) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a2) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a3) ? - Warning - Unrecognized tag - explicit value representation is UN
(0x0009,0x11a1) ? - Warning - Private tag without owner - use owner of parent sequence "TROPHY"
(0x0009,0x11a1) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a2) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a3) ? - Warning - Unrecognized tag - explicit value representation is UN
(0x0009,0x11a1) ? - Warning - Private tag without owner - use owner of parent sequence "TROPHY"
(0x0009,0x11a1) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a2) ? - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0009,0x11a3) ? - Warning - Unrecognized tag - explicit value representation is UN
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9113) Plane Position Sequence - in Per-frame Functional Groups Sequence Item #1
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9116) Plane Orientation Sequence - in Per-frame Functional Groups Sequence Item #1
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9113) Plane Position Sequence - in Per-frame Functional Groups Sequence Item #2
...
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9116) Plane Orientation Sequence - in Per-frame Functional Groups Sequence Item #356
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9113) Plane Position Sequence - in Per-frame Functional Groups Sequence Item #357
Error - Functional Group Sequence already used in Shared Functional Groups Sequence - (0x0020,0x9116) Plane Orientation Sequence - in Per-frame Functional Groups Sequence Item #357
Warning - Value dubious for this VR - (0x0008,0x0090) PN Referring Physician's Name PN [0] = <XXXXXX> - Retired Person Name form
Error - Value invalid for this VR - (0x0020,0x0010) SH Study ID SH [0] = <1.2.250.1.90.1.772081700.1523030489.683> - Length invalid for this VR = 39, expected <= 16
Error - Dicom dataset contains invalid data values for Value Representations
XRay3DCraniofacialImage
Error - Unrecognized enumerated value <RESAMPLED> for value 4 of attribute <Frame Type>
Error - Missing attribute Type 1 Required Element=<PixelPresentation> Module=<CommonCTMRImageDescriptionFrameLevelMacroForXRay3DImage>
....
and other stuff.
I will anonymize the image and will post the link to it.
Thanks.
Roberto Fichera.
Roberto Fichera
May 14, 2018, 7:48:30 AM5/14/18
to Orthanc Users
Hi Sébastien,
here is the link of the image https://www.dropbox.com/s/8kxuzi5bzyz880k/DX000000.dcm?dl=0
Orthanc is currently configured with LoadPrivateDictionary = false because I wasn't able to import certain images due to Endian and also some private tags.
I've also tried to register via Dictionary the above private (0009,11a0) tags, but at moment I wasn't able to make it correctly.
Sébastien Jodogne
May 14, 2018, 9:03:28 AM5/14/18
to Orthanc Users
Hello,
Your DICOM file has "SOPClassUID" set to "1.2.840.10008.5.1.4.1.1.13.1.2", which is a proprietary, non-standard DICOM class by Carestream:
In order to make Orthanc accept such files, you'll have to set its "UnknownSopClassAccepted" configuration option to "true":
HTH,
Sébastien-
PS: For reference, here are the instructions to allow DCMTK's storescu to send such files to Orthanc on Ubuntu 16.04:
# cd /tmp/
# sed 's/^\(PresentationContext125\).*$/\1 = 1.2.840.10008.5.1.4.1.1.13.1.2\\JPEGLossless/' /etc/dcmtk/storescu.cfg > storescu.cfg
# storescu -xf storescu.cfg Default localhost 4242 ./DX000000.dcm
Check out the following page for more information:
Roberto Fichera
May 25, 2018, 1:27:21 PM5/25/18
to Orthanc Users
Hi Sèbastien,
I've tried to set UnknownSopClassAccepted = true, but I still get the same problem
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.398946 main.cpp:1298] Orthanc version: 1.3.2
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.399935 OrthancInitialization.cpp:168] Scanning folder "/etc/orthanc/" for configuration files
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.399976 OrthancInitialization.cpp:120] Reading the configuration from: "/etc/orthanc/orthanc.json"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.400169 OrthancInitialization.cpp:120] Reading the configuration from: "/etc/orthanc/worklists.json"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.400215 OrthancInitialization.cpp:120] Reading the configuration from: "/etc/orthanc/serve-folders.json"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.407317 FromDcmtkBridge.cpp:164] Loading the external DICOM dictionary "/usr/share/dcmtk/dicom.dic"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.413632 FromDcmtkBridge.cpp:164] Loading the external DICOM dictionary "/usr/share/dcmtk/private.dic"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.423836 main.cpp:671] Loading plugin(s) from: /usr/share/orthanc/plugins/
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424013 PluginsManager.cpp:269] Registering plugin 'worklists' (version 1.3.2)
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424025 PluginsManager.cpp:168] Sample worklist plugin is initializing
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424095 PluginsManager.cpp:168] Worklist server is disabled by the configuration file
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424211 PluginsManager.cpp:269] Registering plugin 'serve-folders' (version 1.3.2)
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424350 PluginsManager.cpp:168] ServeFolders: Empty configuration file: No additional folder will be served!
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424363 OrthancInitialization.cpp:1004] SQLite index directory: "/var/lib/orthanc/db-v6"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424460 OrthancInitialization.cpp:1074] Storage directory: "/var/lib/orthanc/db-v6"
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.424704 HttpClient.cpp:691] HTTPS will use the CA certificates from this file: /etc/orthanc/
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425108 ServerScheduler.cpp:135] The server scheduler has started
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425244 LuaContext.cpp:103] Lua says: Lua toolbox installed
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425275 ServerContext.cpp:182] Disk compression is disabled
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425282 ServerIndex.cpp:1403] No limit on the number of stored patients
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425291 ServerIndex.cpp:1420] No limit on the size of the storage area
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.425297 main.cpp:651] Installing the Lua scripts from: /etc/orthanc/send_image.lua
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.426632 main.cpp:863] DICOM server listening with AET ORTHANC on port: 8000
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.426669 MongooseServer.cpp:1075] HTTP compression is enabled
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.427107 main.cpp:796] HTTP server listening on port: 8001
May 25 19:20:49 puma Orthanc[218672]: W0525 19:20:49.427122 main.cpp:683] Orthanc has started
May 25 19:21:04 puma Orthanc[218672]: W: Found element (0009,11a0) with VR UN and undefined length, reading a sequence with transfer syntax LittleEndianImplicit (CP-246)
May 25 19:21:04 puma Orthanc[218672]: W: DcmItem: Length of element (0009,11a1) is odd
May 25 19:21:06 puma Orthanc[218672]: E: DcmElement: PrivateCreator (0dff,00e0) larger (4261412864) than remaining bytes (209010253) in file, premature end of stream
May 25 19:21:06 puma Orthanc[218672]: W: DIMSE Warning: (KPServer,ORTHANC): DIMSE receiveDataSetInMemory: dset->read() Failed (Invalid stream)
May 25 19:21:06 puma Orthanc[218672]: E0525 19:21:06.282193 StoreScp.cpp:294] Store SCP Failed: DIMSE Failed to receive message
Sébastien Jodogne
May 26, 2018, 4:32:12 AM5/26/18
to Orthanc Users
Hello,
I have checked again, and your file works properly.
Here are the full steps to reproduce using Docker. Open a command-line terminal 1:
# cd /tmp/
# sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.3.2
Open a command-line terminal 2:
# cd /tmp/
# sed 's/^\(PresentationContext125\).*$/\1 = 1.2.840.10008.5.1.4.1.1.13.1.2\\JPEGLossless/' /etc/dcmtk/storescu.cfg > storescu.cfg
# storescu -xf storescu.cfg Default localhost 4242 ./DX000000.dcm
I: checking input files ...
I: Requesting Association
I: Association Accepted (Max Send PDV: 16372)
I: Sending file: ./DX000000.dcm
[...]
I: Received Store Response (Success)
I: Releasing Association
The issue is thus to be searched in your DICOM SCU client.
Sébastien-
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