Setting up Orthanc (for dummies)

[thanasis....@gmail.com]

Hello evbdy!
Orthanc is such a great piece of software and I have spent some time trying to figure out what to do without any result.
Sebastien was kind enough to reply to an email and showed me how to install the latest version of Orthanc through docker.
I can now start the service by sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc:1.0.0
I think I located the Configuration file in /home/thanasis/Downloads/Orthanc-1.0.0/Resources and edited the file adding Ginkgo as a DICOM client (hosted for testing purposes on the same computer (running Linux Mint 17.2)
The problems are:
1. Ginkgo cannot PACS Q/R the study uploaded in Orthanc, although the connection test is succesful. I get the message "Failed to perform search:
Query error with PACS Id ORTHANC
Exception in component GIL/PACS :
Unknown Status: 0x686c"

2. I manually uploaded some DICOM pics I have stored locally and when I stop/ start the service the pics do not exist anymore. I think they are not stored or smthg?

3. More problems coming on the way but I would be REALLY grateful if someone could explain to me what to do. I attach the Configuration file

[Robert van Ommen]

1. Try to add ginkgo in orthanc under "DicomModalities" with one of the extra (fourth parameters).

2. Check "StoreDicom" in Configuration.json this should be true.

Regards,

Robert

[thanasis....@gmail.com]

Thanks Robert for your input.
Dicom store is already set to true
fourth parameter is about some specific PAC server protocol. Which one should I choose to use with Orthanc and Ginkgo?

[Robert van Ommen]

Just try them one at a time (make sure you restart orthanc), since I do not have ginkgo.

Maybe try the SyngoVia one first I also needed that one the get QR working without our pacs.

[Sébastien Jodogne]

Hello,

Regarding your question (1), I have made a test with Docker and Ginkgo CADx, and everything runs fine.

For this test, I have used the exact configuration of Ginkgo CADx whose screenshots are in the FAQ, so double check that all the options are properly set:

https://orthanc.chu.ulg.ac.be/book/faq/query-retrieve.html#illustration-ginkgo-cadx

You will find attached to this message the configuration file I used for Orthanc (it is stored as "/tmp/Configuration.json"). WARNINGS:

• The configuration file is the one that is used by the Docker container, with just the "DicomModalities" section updated (cf. https://github.com/jodogne/OrthancDocker).
• You have to adapt the IP address of the "ginkgo" modality in the "DicomModalities" section. This IP address must not be "localhost", as Docker creates a virtual network. Type "ifconfig" at the command line to known the IP address of your computer.
  
• The configuration file you sent has a syntax error (there is a redundant "}," at the end of the "DicomModalities" section).

Then, I started Orthanc as follows:

# sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/Configuration.json:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins:1.0.0

I am then able to Q/R from Orthanc using Ginkgo CADx.

Regarding your question (2), this is entirely normal, as the filesystem of Docker containers is volatile (its content is deleted once the container stops). You can make it persistent by mapping the "/var/lib/orthanc/db" folder of the container to some path in the filesystem of your Linux host, e.g.:

# mkdir /tmp/orthanc-db

# sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/Configuration.json:/etc/orthanc/orthanc.json:ro -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc-plugins:1.0.0

HTH,

Sébastien-

On Wednesday, January 13, 2016 at 12:18:51 PM UTC+1, thanasis....@gmail.com wrote:

[thanasis....@gmail.com]

Thanks everybody for your help.
I am sure this is going to be a... loooong weekend for me trying to put in good use your suggestions. Hope that will be enough,
thanks again!

[thanasis....@gmail.com]

OK, GREAT news! With your suggestions, I managed to make my ultrasound machine to communicate with both Ginkgo and Orthanc! I have not tested connection between Ginkgo and Orthanc due to lack of time but I will do soon.
Sebastien, about the permanent storage of the files: Do I first have to map the "/var/lib/orthanc/db" folder of the container to some path in the Linux filesystem once and then start Orthanc through docker as usual (sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins) ?
Again, many thanks because I think that I am really close to get this to work and this menas a lot for my practice!

[Alain Mazy]

Hi Thanasis,

To map the container path to a linux path, juste use this kind of command:

orthancHostConfigPath="/home/me/orthanc.json"

orthancHostStorage="/home/me/OrthancStorage"

sudo docker run -p 4242:4242 -p 8042:8042 --rm -v $orthancHostStorage:/var/lib/orthanc/db -v $orthancHostConfigPath:/etc/orthanc/orthanc.json:ro jodogne/orthanc-plugins

--

Alain Mazy / CTO 
a...@osimis.io / +32 494 31 67 27

	OSIMIS S.A.  Rue bois Saint-Jean 15/1BE-4102 Seraing  www.osimis.io

[thanasis....@gmail.com]

> OSIMIS S.A. 
> Rue bois Saint-Jean 15/1BE-4102 Seraing 
> www.osimis.io
>  

Cher Alain,
is your suggestion the same with Sebastien's? What's the difference?
# mkdir /tmp/orthanc-db

# sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /tmp/Configuration.json:/etc/orthanc/orthanc.json:ro -v /tmp/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc-plugins:1.0.0

merci beaucoup!

[thanasis....@gmail.com]

So, I created the folder OrthancStorage in /home/thanasis/ to store DICOM files.
My Configuration.json is apparently (?) in /home/thanasis/Λήψεις (this is Downloads in Greek)/Orthanc-1.0.0/Resources

I then give the command sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /home/thanasis/Λήψεις/Orthanc-1.0.0/Resources/Configuration.json:/etc/orthanc/orthanc.json:ro -v /home/thanasis/OrthancStorage/:/var/lib/orthanc/db/ jodogne/orthanc-plugins:1.0.0
W0127 16:36:58.369226 main.cpp:1129] Orthanc version: 1.0.0
W0127 16:36:58.448587 OrthancInitialization.cpp:128] Reading the configuration from: "/etc/orthanc/orthanc.json"
E0127 16:36:58.463881 OrthancInitialization.cpp:617] Only alphanumeric and dash characters are allowed in the names of the modalities
E0127 16:36:58.486624 main.cpp:1169] Uncaught exception, stopping now: [Bad file format] (code 15)
W0127 16:36:58.514131 main.cpp:1202] Orthanc has stopped

apparently with this command orthanc.json is not located.
But the command used so far sudo docker run -p 4242:4242 -p 8042:8042 --rm jodogne/orthanc-plugins works fine. So, what should I do with this error?
Any help is more than welcome!

[Sébastien Jodogne]

According to the log, your problem is not related to the greek localization, but to a syntax error in the content of the configuration file.

In other words, the file "home/thanasis/Λήψεις/Orthanc-1.0.0/Resources/Configuration.json" is not a proper configuration file as "Only alphanumeric and dash characters are allowed in the names of the modalities."

Please read carefully the content of the "DicomModalities" section in your configuration file.

[Alain Mazy]

There's actually no difference.  What I meant is that all you need is this command and there is no need to mount/map anything before issuing the command.

OSIMIS S.A.  Rue bois Saint-Jean 15/1BE-4102 Seraing  www.osimis.io

[thanasis....@gmail.com]

I'm getting closer now!
When using mkdir /home/thanasis/OrthancStorage/orthanc-db and then
sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /home/thanasis/OrthancStorage/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc:1.0.0
I manage to have the database persistent. I just noticed that not all the plugins are enabled. I only have serve-folders and worklist enabled. Do I need the additional ones you think? How can I both have the database persistent and the extra plugins enabled?
Thank you for all your valuable help!

[Sébastien Jodogne]

Simply use the "orthanc-plugins" image instead of "orthanc":

# sudo docker run -p 4242:4242 -p 8042:8042 --rm -v /home/thanasis/OrthancStorage/orthanc-db/:/var/lib/orthanc/db/ jodogne/orthanc-plugins:1.0.0

[thanasis....@gmail.com]

For now I'm happy with the way things seem to work.
After a lot of try-and-error sessions I realised that (very often) my GE ultrasound fails to connect to both Orthanc or Gingo. I then have to restart GE machine and then it can connect. This was the reason I was telling you that I cannot connect while all configuration was fine. I do not know why this is happening.
When I find time I will try to set up a dedicated Orthanc server with plenty of space and see how it goes!
Thanks for all the valuable help again

[Sébastien Jodogne]

Fine, glad to read that your problem is solved!