Orthanc failed to transcode

General
1

Hi Author,
I have dicom (see in the attachment) and upload to Orthanc via UI. When I use dicomweb to retrieve the instance : curl -i -uorthanc:orthanc localhost:8042/wado-rs/studies/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.5.0/series/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.4.0/instances/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.9.0 . Orthanc throws exception as below

I1017 11:13:50.297123 HttpServer.cpp:1262] (http) GET /wado-rs/studies/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.5.0/series/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.4.0/instances/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.9.0
I1017 11:13:50.297354 OrthancPlugins.cpp:2447] (plugins) Delegating HTTP request to plugin for URI: /wado-rs/studies/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.5.0/series/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.4.0/instances/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.9.0
I1017 11:13:50.297448 OrthancPlugins.cpp:4009] (plugins) Plugin making REST POST call to URI /tools/find (after plugins)
I1017 11:13:50.300685 ServerContext.cpp:1487] Number of candidate resources after fast DB filtering on main DICOM tags: 1
I1017 11:13:50.300994 ServerContext.cpp:1635] Number of matching resources: 1
I1017 11:13:50.301127 OrthancPlugins.cpp:3172] (plugins) Plugin making REST GET call on URI /instances/8febf686-10972e55-1d81daf1-7d873794-a8dff850/metadata/TransferSyntax (built-in API)
I1017 11:13:50.301269 OrthancPlugins.cpp:3172] (plugins) Plugin making REST GET call on URI /instances/8febf686-10972e55-1d81daf1-7d873794-a8dff850/file (built-in API)
I1017 11:13:50.301370 FilesystemStorage.cpp:161] Reading attachment "1d274ef8-6036-4eeb-b66d-f27bd1d82e50" of "DICOM" content type
I1017 11:13:50.502627 DcmtkTranscoder.cpp:306] DCMTK transcoding from 1.2.840.10008.1.2.4.91 to one of: 1.2.840.10008.1.2.1
E1017 11:13:50.502736 OrthancException.cpp:61] Not implemented yet: Cannot transcode image
E1017 11:13:50.506122 PluginsErrorDictionary.cpp:100] Exception inside the plugin engine: Error encountered within the plugin engine
^CI1017 11:14:09.547477 LuaJobManager.cpp:98] (lua) Awaking trailing sleep
I1017 11:14:09.547547 LuaScripting.cpp:900] Stopping the Lua engine
I1017 11:14:09.647805 LuaScripting.cpp:906] The Lua engine has stopped
W1017 11:14:09.647873 main.cpp:985] Orthanc is stopping
I1017 11:14:09.728883 OrthancWebDav.cpp:1707] Stopping the WebDAV upload thread

With dcm4chee, I can get the instance with that URL. Can you please help to check what’s wrong with Orthanc ?

P/S : I am using the Orthanc version 1.12.1, DicomWeb 1.15. And this is my configuration: orthanc.json - Google Drive

Thanks,
Chris

2

Hi,

Your image is in JP2K → DCMTK is not able to decode it, you need to enable the GDCM plugin. However, even with GDCM, I’m encountering an error in GDCM code here that states that the file is invalid:

image
image1276×159 10.8 KB

When trying to open the file in Radiant, it crashes Radiant :frowning:

And there are errors detected with dciodvfy:

dciodvfy DCM_0.dcm
(0x0008,0x0017)  ?  - Warning - Unrecognized tag - assuming explicit value representation OK
(0x0008,0x0019)  ?  - Warning - Unrecognized tag - assuming explicit value representation OK
Warning - Missing attribute or value that would be needed to build DICOMDIR - Patient ID
Warning - Missing attribute or value that would be needed to build DICOMDIR - Study ID
Warning - Missing attribute or value that would be needed to build DICOMDIR - Series Number
VLWholeSlideMicroscopyImage
Error - Value is zero for value 1 of attribute <Slice Thickness>
Error - Value is zero for value 1 of attribute <Imaged Volume Depth>
Error - Attribute with an even group number is not a recognized standard attribute - (0x0008,0x0017)  ?
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x0017)  ?
Error - Attribute with an even group number is not a recognized standard attribute - (0x0008,0x0019)  ?
Warning - Attribute is not present in standard DICOM IOD - (0x0008,0x0019)  ?
Warning - Dicom dataset contains attributes not present in standard DICOM IOD - this is a Standard Extended SOP Class

So I don’t think I’ll investigate any further :slight_smile:

Best regards,

Alain.

3

Thanks Alain,

I am surprise that DCM4CHEE is still able to handle this case.
curl -i http://localhost:18080/dcm4chee-arc/aets/DCM4CHEE/rs/studies/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.5.0/series/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.4.0/instances/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.9.0

image
image924×504 63.3 KB

Actually this this the Pathology Image dicom file. Orthanc can display the file if I am using Whole Slide Imaging plugin. However I am using another viewer which requires to get the file via Wado-RS API. May the Orthanc improve the decoding or at least return the file without decoding via Wado-RS API ?

4

That does it:
curl-output /tmp/out.dcm -H "accept: multipart/related;type=application/dicom;transfer-syntax=*" localhost:8043/dicom-web/studies/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.5.0/series/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.4.0/instances/1.3.6.1.4.1.5962.99.1.3073532328.211211830.1686700745128.9.0