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MONAI Label: The OHIF flow as described in the README does not work #594
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Can you please raise this over MONAI Label github repo.. Feels like some step you have missed.. otherwise multiple people have tried running MONAI Label over OHIF (given you have setup for dicomweb e.g. orthanc) @diazandr3s can you please help |
Hi @patricio-astudillo, thanks for raising this issue. Which web explorer are you using to open OHIF? I saw sometimes Firefox doesn't load OHIF? I guess it is a cookies issue. Can you please try opening OHIF with Google Chrome? http://127.0.0.1:8000/ohif |
Hey, Prepare environment:
Install: fails due to:
Try again with a different python version: Prepare environment:
pip install monailabel
monailabel apps --download --name deepedit --output apps
monailabel datasets --download --name Task09_Spleen --output datasets
Now I can go to 127.0.0.1:8000 and see; sudo apt-get install orthanc orthanc-dicomweb monailabel start_server --app apps/deepedit --studies http://127.0.0.1:8042/dicom-web |
Thanks for the detailed response, this is helpful :) You've already downloaded the dataset in NIFTI format. But if you'd like to use OHIF, they need to be uploaded in Orthanc. Here are the instructions to convert images from NIFTI to DICOM: https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif This is essentially the reason you can't see studies in OHIF. Once you load them in Orthanc, you should be able to see them in OHIF. Please let us know how this goes :) |
Hi @diazandr3s, You are welcome and thanks for your advice however, I've uploaded the DICOM of a single patient to the Orthanc server. I've blocked it with a white rectangle for privacy reasons. However, I tried to replicate the bug this morning and now the loading works for some reason. However, when I want to enable the MONAI label panel, I receive the following error: |
Would it be possible to see the logs? You can find them in the logs folder or at http://127.0.0.1:8000/logs If it helps, I'm happy to schedule a meeting and talk about the use case. Please let us know |
Dear @diazandr3s , Thanks for the quick response, I've contacted you through linked-in to organise a meeting. Best regards, |
Superb! |
Hi, I worked with @diazandr3s on this issue and we managed to resolve this. Thanks |
Superb! |
@patricio-astudillo @diazandr3s How did you resolve this issue? When I go to localhost:8000/ohif/ I'm seeing a blank page I have loaded images on Orthanc and can see them at localhost:8042 |
It is great to see you're using MONAI Label. Can I ask you whether you're using the Docker container? I've just checked and it seems to work smoothly when using Docker: ohif.mp4Please let us know |
How you have installed monailabel? |
Hi,
nice that you use Monai Label, this was caused by not following the
installation procedure (and make sure all previous monai / monai label /
monai deploy packages are removed or start from a vanilla environment)
Best of luck,
Patricio
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You might be using github way of monailabel.. in that case, you have to build OHIF explicitly...
https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif#development-setup Easy way is run PIP Install MONAILabel or use MONAILabel Docker |
@diazandr3s @patricio-astudillo @SachidanandAlle Thanks so much for all your help! I'm using the docker version of MONAI, but I still can't seem to get it to work. I'm running on macOS 12. I followed @diazandr3s procedure but when I open http://0.0.0.0/8000 I can't connect to the webpage. |
http://0.0.0.0/8000 ? First.. it's http://0.0.0.0:8000 for Server APIs.. and http://0.0.0.0:8000/ohif for OHIF interface.. If you can share the command which you are running to start the server and the logs... that can be more helpful for others to suggest what's wrong... If you are using docker sometimes you need to open up the port for host container as well.. and sometimes the loopback address.. |
My apologies, I meant http://0.0.0.0:8000/ The commands I run are -
Connecting to http://0.0.0.0:8000/ Connecting to http://0.0.0.0:8000/ohif/ Connecting to http://127.0.0.1:8042 opens Orthanc where I have one patient's DICOM image data Logs:
|
I can confirm that I discovered the same behavior on macOS when running: docker run --rm -ti --ipc=host --net=host projectmonai/monailabel:latest bash
# inside docker container:
monailabel apps --download --name radiology --output apps
monailabel start_server --app apps/radiology --studies http://127.0.0.1:8042/dicom-web --conf models deepedit MONAILabel, OHIF and Orthanc all are then not reachable using 'http://127.0.0.1:8000' or 'http://127.0.0.1:8000/ohif' or 'http://127.0.0.1:8042'. I was able to get MONAILabel up using: docker run --rm -ti --ipc=host -p 8000:8000 -p 8042:8042 projectmonai/monailabel:latest bash
# inside docker container:
monailabel apps --download --name radiology --output apps
monailabel start_server --app apps/radiology --studies http://127.0.0.1:8042/dicom-web --conf models deepedit But in this case Orthanc and OHIF are not reachable. Investigating the container, Orthanc does not get started... |
First thing.. you need GPUS.. without that monailabel is not complete.. you can run, but at the end most of the features won't be supported without GPU.. Second.. I see you are trying 0.0.0.0 (in some cases.. you should try 127.0.0.1:8000 instead.. depends on the resolve)
otherwise logs are good.. 2nd thing.. when u start the server Third.. Orthanc is not part of monailabel (its a separate thing).. due to license, it can be part of Monailabel.. |
Thanks for clarification, @SachidanandAlle. These lines should perhaps be removed, as they imply that the MONAILabel docker image ships with Orthanc included ... Lines 37 to 46 in fb8d047
|
@adwaykanhere, my current workaround is that I am running a fully-configured Orthanc docker container next to a MONAILabel docker container. Works great... |
Thanks a lot, @jlvahldiek How are you able to connect the MONAILabel docker to OHIF via Orthanc? |
@SachidanandAlle 127.0.0.1:8000 also does not work for MacOS |
@adwaykanhere, I will work on a tutorial setting up all three with Docker, probably will be published in a couple of days. If you can't wait please contact me directly... |
Hi @adwaykanhere, MONAI Label needs GPUs to work - It hasn't been tested/doesn't work on macOS. and then connect to it using OHIF/Slicer from your macOS machine. Hope this helps, |
The OHIF flow as described in the README does not work. I have followed the instructions and tried to get OHIF up and running, but it does not work. Can anyone confirm that this flow is currently not working or update the README file?
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