OHIF - Submit Label but get Exception in ASGI application (500 Internal Server Error)

[tkt9k2562]

Hi there ,

I cannot submit the label , while it return me ASGI application (500 Error)

My environment is ubuntu 20.04 , install cuda & anaconda (python 3.9) ,
and git clone this main branch (Development version) ,

My steps are:

• Fist , use 'Scribbles' to label (plot) the dicom file
• Then , press 'Submit Label' button

Then I see it returns me Exception in ASGI application (500 Error)

And the server prints these

[2022-09-10 07:16:12,257] [66358] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/cors.py", line 92, in __call__
    await self.simple_response(scope, receive, send, request_headers=headers)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/cors.py", line 147, in simple_response
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 210, in api_save_label
    return save_label(background_tasks, image, params, tag, label, user.username)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 113, in save_label
    label_id = instance.datastore().save_label(image, label_file, tag, save_params)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/dicom.py", line 167, in save_label
    image_uri = self.get_image_uri(image_id)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/dicom.py", line 80, in get_image_uri
    dicom_web_download_series(None, image_id, image_dir, self._client, self._fetch_by_frame)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/utils/dicom.py", line 81, in dicom_web_download_series
    instances = client.retrieve_series(study_id, series_id)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/dicomweb_client/web.py", line 2319, in retrieve_series
    self._get_series(
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/dicomweb_client/web.py", line 2262, in _get_series
    return self._http_get_multipart_application_dicom(
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/dicomweb_client/web.py", line 1078, in _http_get_multipart_application_dicom
    response = self._http_get(
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/dicomweb_client/web.py", line 619, in _http_get
    response.raise_for_status()
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/requests/models.py", line 1021, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http://35.185.175.228:8042/dicom-web//studies/1.2.840.113619.6.44.184007267965399520897507264631124794427/series/1.2.840.113619.2.80.2406849009.24510.1601261495.2.2

I am not sure if the steps I did were wrong , or maybe any requirements for the dicom file ?

Does anyone have any ideas?

Thanks in advance!

[tkt9k2562]

Event If I press the Scribbles 'Run' button

I get the same error - ASGI application (500 Error)

Would you give me some advice , I have no idea ><

Thanks in advance !

[diazandr3s]

Hi @tkt9k2562,

Can I ask you which DICOM Web server you're using? Is it Orthanc? It seems MONAI Label can't reach the DICOM Web server.
On the dataset side, is this a single MR modality?

Please let us know

[tkt9k2562]

Yes , I use single Orthanc on localhost.
But I am not sure is there need any setting about MR modality ?

I install Orthanc on Ubuntu 20.04 follow this

sudo apt install orthanc
sudo apt install orthanc-dicomweb
sudo apt install orthanc-webviewer
sudo apt install orthanc-postgresql

Then I run Monailabel-OHIF

cd plugins/ohif && ./build.sh
monailabel start_server -a apps/radiology -s http://127.0.0.1:8042/dicom-web --conf models segmentation_spleen

the /etc/orthanc/dicomweb.json is below

{
    /**
     * The following options control the configuration of the Orthanc
     * plugin adding support of WADO and DICOMweb.
     **/

    "DicomWeb" : {
        "Enable" : true,         // Whether DICOMweb support is enabled
        "Root" : "/dicom-web/",  // Root URI of the DICOMweb API (for QIDO-RS, STOW-RS and WADO-RS)
        "EnableWado" : true,     // Whether WADO-URI (aka. WADO) support is enabled
        "WadoRoot" : "/wado",    // Root URI of the WADO-URI (aka. WADO) API
        "Host" : "localhost",    // Hard-codes the name of the host for subsequent WADO-RS requests
        "Ssl" : false            // Whether HTTPS should be used for subsequent WADO-RS requests
    }
}

And I don't modify the default orthanc DicomModalities , which is empty

// /etc/orthanc/orthanc.json

"DicomModalities" : {
    // "sample" : [ "STORESCP", "127.0.0.1", 2000 ]
}

Should I need to add something like the site ?
Or maybe something like "ohif" : [ "OHIFDCM", "localhost", 3000 ] the site ?

If you need other information , please tell me
Thank you~

[tkt9k2562]

the text of my /etc/orthanc/orthanc.json is like this

orthanc.txt

[tkt9k2562]

And I don't use any database (e.g Pgsql) yet

[diazandr3s]

Thanks for the update, @tkt9k2562.

So both MONAI Label server and Orthanc are running on localhost, right?

Not sure why I'm seeing this in the error logs:

requests.exceptions.HTTPError: 500 Server Error: Internal Server Error for url: http://35.185.175.228:8042/dicom-web//studies/1.2.840.113619.6.44.184007267965399520897507264631124794427/series/1.2.840.113619.2.80.2406849009.24510.1601261495.2.2

Have you tried with the MONAI Label Docker image? It comes with all the set-up: https://github.com/Project-MONAI/MONAILabel/blob/main/Dockerfile

Please let us know

[tkt9k2562]

Yes , I run both MONAI Label server and Orthanc are on localhost.

35.185.175.228 is the external IP , which is the host I rent on GCP.

Let me try the MONAI Label Docker image ~

[SachidanandAlle]

Default orthanc server is not having some diocmweb implementation.. so u need to upgrade it.. the steps are mentioned here for reference:
https://github.com/Project-MONAI/MONAILabel/tree/main/plugins/ohif#installing-orthanc-dicomweb

[tkt9k2562]

Thank you! I miss the step.

I follow this to upgrade to latest version of Orthanc and its plugin.

And I modify DicomModalities in my case and restart it (not use docker)
("35.185.175.228" is the external ip of my host)

cd /home/tkt9k2562/MONAILabel/plugins/ohif
monailabel start_server -a apps/radiology -s http://35.185.175.228:8042/dicom-web --conf models segmentation_spleen

  "DicomModalities" : {
    /**
     * Uncommenting the following line would enable Orthanc to
     * connect to an instance of the "storescp" open-source DICOM
     * store (shipped in the DCMTK distribution) started by the
     * command line "storescp 2000".
     **/
    "sample" : ["MONAILABEL", "35.185.175.228", 104]

But there still an error ><
However it seems different - No such file or directory: '/tmp/tmpgiuc5_ft.dcm'

[2022-09-14 10:43:06,549] [81542] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/cors.py", line 92, in __call__
    await self.simple_response(scope, receive, send, request_headers=headers)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/middleware/cors.py", line 147, in simple_response
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 210, in api_save_label
    return save_label(background_tasks, image, params, tag, label, user.username)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 113, in save_label
    label_id = instance.datastore().save_label(image, label_file, tag, save_params)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/dicom.py", line 182, in save_label
    label_series_id = dicom_web_upload_dcm(label_file, self._client)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/utils/dicom.py", line 116, in dicom_web_upload_dcm
    dataset = dcmread(input_file)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/pydicom/filereader.py", line 993, in dcmread
    fp = open(fp, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpgiuc5_ft.dcm'

Would you have any idea ?

Thanks in advance!

[tkt9k2562]

Here provides the dicom I use as this , and when submit label it will get

File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 210, in api_save_label
    return save_label(background_tasks, image, params, tag, label, user.username)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/endpoints/datastore.py", line 113, in save_label
    label_id = instance.datastore().save_label(image, label_file, tag, save_params)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/dicom.py", line 182, in save_label
    label_series_id = dicom_web_upload_dcm(label_file, self._client)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/monailabel/datastore/utils/dicom.py", line 116, in dicom_web_upload_dcm
    dataset = dcmread(input_file)
  File "/home/tkt9k2562/anaconda3/lib/python3.9/site-packages/pydicom/filereader.py", line 993, in dcmread
    fp = open(fp, 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp7zv16n9m.dcm'

image-00074.zip

[diazandr3s]

Thanks for the update @tkt9k2562.
If both Orthanc and MONAI Label servers are on the same PC as you mentioned previously, no need to specify the public IP. Please run the following command and let us know:

monailabel start_server -a apps/radiology -s http://localhost:8042/dicom-web --conf models segmentation_spleen

the command you were running should work as well. But my guess is that ports are closed on that machine so the server is not visible to the internet.

Hope this helps,

[tkt9k2562]

Thank you!
Let me try later and check the firewall of my machine ports
(I were tied up in other things these days ><)

[tkt9k2562]

I check my ports , but it still doesn't work

However , I cannot figure out where the problem is.

Let me mark the issue resolved and try the provided MONAI Label Docker image.

Thank you all !

[YuanSingapore]

@tkt9k2562, based on my experience, the error is due to the original DICOM file, which does not conform the DICOM standard. It happened when MONAILabel is trying to convert from NIFTI to DICOM but some fields are not right, or empty, this error will appear.
@diazandr3s, is there a way to correct the header information in MONAI so that it doesn't become a blocker for clinicians? Many thanks