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    Matvey Ezhov
    @ematvey
    Greetings. I'm trying to upload a multi-file CBCT (volumetric) DICOM to demo instance, and receiving errors for all instances to test the tool. Is it because such use case is not supported, or because of the limitation of demo instance?
    image.png
    CSV error log is not very helpful.
    Nghia
    @Lego1st

    Greetings. I'm trying to upload a multi-file CBCT (volumetric) DICOM to demo instance, and receiving errors for all instances to test the tool. Is it because such use case is not supported, or because of the limitation of demo instance?

    Yes. Currently, the Demo instance is limited to view-only mode. FYI, VinDr Lab supports multi-file DICOM upload.

    Matvey Ezhov
    @ematvey
    Sounds great, trying it now. Can you share your vision around 3D annotation workflow?
    Like, MITK does it mainly by drawing multiple polygons and interpolating between slices, ITK-SNAP uses 3D brushes to draw masks, 3D Slicer has a whole suite of tools but is a nightmare to use. Of them only ITK-SNAP doesn't crash constantly in my experience.
    Nghia
    @Lego1st
    We have implemented this 3D annotation internally. At the first step, we have interpolated slices with keyframes. I also plan to implement some essential tools that support editing these 3D annotations.
    Matvey Ezhov
    @ematvey
    Inside MPR? I'm curious to test it.
    Nghia
    @Lego1st
    Yes, in MPR view.
    We will have a plan to release it if it is mature enough :D. I hope to hear more ideas from the community as well.
    Matvey Ezhov
    @ematvey
    Interpolation with keyframes sounds reasonable for the first try.
    I've thought for a long time about the UX for 3D annotation. But it's so hard for humans to think and annotate in volumes. 3D brush is fun to use but not very efficient.
    btw I've tried to deploy locally, but vinlab-api is restarting.
    (base) ➜  docker git:(master) docker-compose ps
          Name                    Command                 State                           Ports
    -----------------------------------------------------------------------------------------------------------------
    vinlab-api         ./bin                            Restarting
    vinlab-dashboard   docker-entrypoint.sh ./run.sh    Up           0.0.0.0:57679->80/tcp
    vinlab-es          /tini -- /usr/local/bin/do ...   Up           0.0.0.0:57698->9200/tcp, 9300/tcp
    vinlab-idgen       ./bin                            Up           0.0.0.0:57677->8080/tcp
    vinlab-keycloak    /opt/jboss/tools/docker-en ...   Up           8080/tcp, 8443/tcp, 0.0.0.0:57676->9090/tcp
    vinlab-minio       /usr/bin/docker-entrypoint ...   Up           0.0.0.0:57671->9000/tcp
    vinlab-nginx       /docker-entrypoint.sh ngin ...   Up           80/tcp, 0.0.0.0:8080->8080/tcp
    vinlab-orthanc     /docker-entrypoint.sh /tmp ...   Up           0.0.0.0:57668->4242/tcp, 0.0.0.0:57669->8042/tcp
    vinlab-redis       docker-entrypoint.sh redis ...   Up           0.0.0.0:57670->6379/tcp
    vinlab-rqlite      docker-entrypoint.sh rqlit ...   Up           0.0.0.0:57673->4001/tcp, 0.0.0.0:57674->4002/tcp
    vinlab-uploader    ./run.sh                         Up           0.0.0.0:57682->8080/tcp
    vinlab-viewer      docker-entrypoint.sh ./run.sh    Up           443/tcp, 0.0.0.0:57681->80/tcp
    Matvey Ezhov
    @ematvey
    Seems to be related to mounting docker/permissions.csv
    Nghia
    @Lego1st
    You try Docker option, right ?
    Matvey Ezhov
    @ematvey
    yep
    Nghia
    @Lego1st
    Oh, please try Kubernetes option instead. It seems that there is an issue that made Docker optiontemporarily not available now. We are working on this issue. @iamatsundere Do you have any idea ?
    Matvey Ezhov
    @ematvey
    this one
    2021/04/06 16:05:57 [INFO] [main.go:75] API is running in [production] mode
    2021/04/06 16:05:57 [INFO] [main.go:96] [http://vinlab-es:9200]
    panic: Cannot connect to ES
    goroutine 1 [running]:
    main.main()
    /opt/app/main.go:103 +0x20a5
    simisimi
    @iamatsundere
    The API need a little bit of time to start, because of waiting for ES. But we recommend you to use Kubernetes instead while we fixing the issue of Docker deployment.
    Matvey Ezhov
    @ematvey
    I'll try that thanks
    simisimi
    @iamatsundere
    @ematvey yeah, ping us if it works (or you need any support) :))
    Matvey Ezhov
    @ematvey
    Great, thanks!
    Can you share your estimates for when 3D annotation will be released?
    I get that it'll be done when it's done) but what do you think? We only need 3D annotation...
    Matvey Ezhov
    @ematvey
    Seems to be a typo in k8s doc: vinbigdata-medical/vindr-lab#1
    Matvey Ezhov
    @ematvey
    Nope, something's not right with the namespaces still.
    Events:
      Type     Reason       Age                  From               Message
      ----     ------       ----                 ----               -------
      Normal   Scheduled    19m                  default-scheduler  Successfully assigned default/apigateway-deployment-d6dcc5d8f-kngb6 to minikube
      Warning  FailedMount  8m43s (x2 over 13m)  kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[default-token-vq7vz apigateway-configmap]: timed out waiting for the condition
      Warning  FailedMount  118s (x6 over 17m)   kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[apigateway-configmap default-token-vq7vz]: timed out waiting for the condition
      Warning  FailedMount  86s (x17 over 19m)   kubelet            MountVolume.SetUp failed for volume "apigateway-configmap" : configmap "apigateway-configmap" not found