MONAILabel server not responding and given this error: [25188] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting. #1526

VSPuzzler · 2023-08-17T23:11:53Z

VSPuzzler
Aug 17, 2023

Hello I am trying to start a server on my windows 10 laptop (doesn't have CUDA, but I assume it will still work just slower). I have followed the steps to use MONAILabel on 3DSlicer, but I am having issues starting the server. I run this command in command prompt: monailabel start_server --app radiology --studies Task02_Heart/imagesTr
I then get this error:

Using PYTHONPATH=C:\Program Files;
""
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: app = C:\Users\vinee\radiology
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: studies = C:\Users\vinee\Task02_Heart\imagesTr
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: conf = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: root_path = /
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2023-08-16 21:10:23,998] [10412] [MainThread] [INFO] (__main__:296) -
Allow Origins: ['*']
[2023-08-16 21:10:24,785] [10412] [MainThread] [INFO] (uvicorn.error:74) - Started server process [10412]
[2023-08-16 21:10:24,785] [10412] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2023-08-16 21:10:24,785] [10412] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: C:\Users\vinee\radiology; studies: C:\Users\vinee\Task02_Heart\imagesTr; conf: {}
[2023-08-16 21:10:24,911] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-08-16 21:10:24,942] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-08-16 21:10:24,942] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-08-16 21:10:24,944] [10412] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>

---------------------------------------------------------------------------------------
Provide --conf models <name>
Following are the available models.  You can pass comma (,) seperated names to pass multiple
    all, deepedit, deepgrow_2d, deepgrow_3d, localization_spine, localization_vertebra, segmentation, segmentation_spleen, segmentation_vertebra
---------------------------------------------------------------------------------------

[2023-08-16 21:10:24,944] [10412] [MainThread] [ERROR] (uvicorn.error:123) - Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 677, in lifespan
    async with self.lifespan_context(app) as maybe_state:
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 566, in __aenter__
    await self._router.startup()
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 654, in startup
    await handler()
  File "C:\Program Files\Python38\lib\site-packages\monailabel\app.py", line 108, in startup_event
    instance = app_instance()
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\utils\app.py", line 50, in app_instance
    app = c(app_dir=app_dir, studies=studies, conf=conf)
  File "C:\Users\vinee\radiology\main.py", line 65, in __init__
    exit(-1)
  File "C:\Program Files\Python38\lib\_sitebuiltins.py", line 26, in __call__
    raise SystemExit(code)
SystemExit: -1

[2023-08-16 21:10:24,958] [10412] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.

C:\Users\vinee>https://docs.monai.io/projects/label/en/0.1.0/quickstart.html
'https:' is not recognized as an internal or external command,
operable program or batch file.

C:\Users\vinee>monailabel start_server --app deepedit_left_atrium --studies Task02_Heart/imagesTr
Using PYTHONPATH=C:\Program Files;
""
APP Directory deepedit_left_atrium NOT Found

C:\Users\vinee>monailabel start_server --app radiology --studies Task02_Heart/imagesTr
Using PYTHONPATH=C:\Program Files;
""
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: version = False
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: app = C:\Users\vinee\radiology
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: studies = C:\Users\vinee\Task02_Heart\imagesTr
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: verbose = INFO
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: conf = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: host = 0.0.0.0
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: port = 8000
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: uvicorn_app = monailabel.app:app
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: ssl_certfile = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: ssl_keyfile_password = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: ssl_ca_certs = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: workers = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: limit_concurrency = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: access_log = False
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: root_path = /
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: log_level = info
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: log_config = None
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: dryrun = False
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:285) - USING:: action = start_server
[2023-08-17 19:07:12,543] [25188] [MainThread] [INFO] (__main__:296) -
Allow Origins: ['*']
[2023-08-17 19:07:13,429] [25188] [MainThread] [INFO] (uvicorn.error:74) - Started server process [25188]
[2023-08-17 19:07:13,429] [25188] [MainThread] [INFO] (uvicorn.error:48) - Waiting for application startup.
[2023-08-17 19:07:13,429] [25188] [MainThread] [INFO] (monailabel.interfaces.utils.app:37) - Initializing App from: C:\Users\vinee\radiology; studies: C:\Users\vinee\Task02_Heart\imagesTr; conf: {}
[2023-08-17 19:07:13,691] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-08-17 19:07:13,710] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-08-17 19:07:13,710] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-08-17 19:07:13,710] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-08-17 19:07:13,710] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-08-17 19:07:13,718] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-08-17 19:07:13,719] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-08-17 19:07:13,719] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-08-17 19:07:13,719] [25188] [MainThread] [INFO] (monailabel.utils.others.class_utils:57) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>

---------------------------------------------------------------------------------------
Provide --conf models <name>
Following are the available models.  You can pass comma (,) seperated names to pass multiple
    all, deepedit, deepgrow_2d, deepgrow_3d, localization_spine, localization_vertebra, segmentation, segmentation_spleen, segmentation_vertebra
---------------------------------------------------------------------------------------

[2023-08-17 19:07:13,727] [25188] [MainThread] [ERROR] (uvicorn.error:123) - Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 677, in lifespan
    async with self.lifespan_context(app) as maybe_state:
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 566, in __aenter__
    await self._router.startup()
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 654, in startup
    await handler()
  File "C:\Program Files\Python38\lib\site-packages\monailabel\app.py", line 108, in startup_event
    instance = app_instance()
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\utils\app.py", line 50, in app_instance
    app = c(app_dir=app_dir, studies=studies, conf=conf)
  File "C:\Users\vinee\radiology\main.py", line 65, in __init__
    exit(-1)
  File "C:\Program Files\Python38\lib\_sitebuiltins.py", line 26, in __call__
    raise SystemExit(code)
SystemExit: -1

[2023-08-17 19:07:13,727] [25188] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting.

Does anyone know what is wrong?

Answered by diazandr3s

Aug 19, 2023

Hi @VSPuzzler,

It seems you don't have annotated samples to train the model. This is what I'm seeing from the logs:

ValueError: num_samples should be a positive integer value, but got num_samples=0

Did you organize the volumes as shown here or here? Are you using NIfTI or DICOM format?

If using DICOM format, you have to use a DICOM Web server. Otherwise, images have to be converted to NIfTI.

Hope this helps,

View full answer

tangy5 · 2023-08-17T23:15:31Z

tangy5
Aug 17, 2023
Maintainer

Hi, the command is not complete,

you will need to add a model name to start monailabel command: ex.g,
monailabel start_server --app radiology --studies Task02_Heart/imagesTr --conf models deepedit
But note here, we current don't have a pre-trained model for segmenting Task02 heart MRI data, you will need to provide your own pre-trained model.

4 replies

VSPuzzler Aug 18, 2023
Author

Hello, where can I find the list of tasks that MONAILabel can do? I am trying to segment arteries from MRA data.

diazandr3s Aug 18, 2023
Maintainer

Hi @VSPuzzler,

These are the currently available models in MONAI Label (https://github.com/Project-MONAI/MONAILabel/tree/main/sample-apps/radiology#pretrained-models) and in the MONAI Model Zoo (https://github.com/Project-MONAI/model-zoo/tree/dev/models)

I'm not sure there is a model for brain arteries segmentation using MRA. However, if you have labels, you may find this video useful to create your own model: https://youtu.be/3HTh2dqZqew

Hope this helps,

VSPuzzler Aug 19, 2023
Author

Hello, Thank you for the help. I will try that. I click train in 3d slicer on a test picture to make sure everything is working but this appears:

Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\runpy.py", line 193, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\Program Files\Python38\lib\runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\utils\app.py", line 128, in <module>
    run_main()
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\utils\app.py", line 113, in run_main
    result = a.train(request)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\app.py", line 423, in train
    result = task(request, self.datastore())
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\train\basic_train.py", line 466, in __call__
    res = self.train(0, world_size, req, datalist)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\train\basic_train.py", line 544, in train
    context.trainer = self._create_trainer(context)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\train\basic_train.py", line 696, in _create_trainer
    train_data_loader=self.train_data_loader(context),
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\train\basic_train.py", line 267, in train_data_loader
    return self._dataloader(context, dataset, context.train_batch_size, num_workers, shuffle)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\train\basic_train.py", line 248, in _dataloader
    return ThreadDataLoader(
  File "C:\Program Files\Python38\lib\site-packages\monai\data\thread_buffer.py", line 193, in __init__
    super().__init__(dataset, **kwargs)
  File "C:\Program Files\Python38\lib\site-packages\monai\data\dataloader.py", line 91, in __init__
    super().__init__(dataset=dataset, num_workers=num_workers, **kwargs)
  File "C:\Program Files\Python38\lib\site-packages\torch\utils\data\dataloader.py", line 351, in __init__
    sampler = RandomSampler(dataset, generator=generator)  # type: ignore[arg-type]
  File "C:\Program Files\Python38\lib\site-packages\torch\utils\data\sampler.py", line 107, in __init__
    raise ValueError("num_samples should be a positive integer "
ValueError: num_samples should be a positive integer value, but got num_samples=0
[2023-08-18 20:24:21,738] [26416] [ThreadPoolExecutor-2_0] [INFO] (monailabel.utils.async_tasks.utils:83) - Return code: 1
[2023-08-18 20:26:04,731] [26416] [MainThread] [INFO] (monailabel.endpoints.infer:161) - Infer Request: {'model': 'Histogram+GraphCut', 'image': '3D_TOF_MRA', 'label': 'C:\\Users\\vinee\\AppData\\Local\\Temp\\tmpo40s20ba.nii.gz', 'num_bins': 64, 'lamda': 1.0, 'sigma': 0.1, 'device': 'cpu', 'roi': [], 'label_info': [{'name': 'background', 'id': 1}, {'name': 'spleen', 'id': 2}, {'name': 'right kidney', 'id': 3}, {'name': 'left kidney', 'id': 4}, {'name': 'liver', 'id': 5}, {'name': 'stomach', 'id': 6}, {'name': 'aorta', 'id': 7}, {'name': 'inferior vena cava', 'id': 8}, {'name': 'background_scribbles', 'id': 9}, {'name': 'foreground_scribbles', 'id': 10}], 'selected_label_name': 'spleen', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2023-08-18 20:26:04,734] [26416] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:277) - Infer Request (final): {'num_bins': 64, 'lamda': 1.0, 'sigma': 0.1, 'device': 'cpu', 'model': 'Histogram+GraphCut', 'image': '', 'label': 'C:\\Users\\vinee\\AppData\\Local\\Temp\\tmpo40s20ba.nii.gz', 'roi': [], 'label_info': [{'name': 'background', 'id': 1}, {'name': 'spleen', 'id': 2}, {'name': 'right kidney', 'id': 3}, {'name': 'left kidney', 'id': 4}, {'name': 'liver', 'id': 5}, {'name': 'stomach', 'id': 6}, {'name': 'aorta', 'id': 7}, {'name': 'inferior vena cava', 'id': 8}, {'name': 'background_scribbles', 'id': 9}, {'name': 'foreground_scribbles', 'id': 10}], 'selected_label_name': 'spleen', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz', 'description': 'A post processing step with histogram-based GraphCut for Generic segmentation'}
monai.transforms.io.dictionary LoadImaged.__init__:image_only: Current default value of argument `image_only=False` has been deprecated since version 1.1. It will be changed to `image_only=True` in version 1.3.
[2023-08-18 20:26:04,740] [26416] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2023-08-18 20:26:04,741] [26416] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['num_bins', 'lamda', 'sigma', 'device', 'model', 'image', 'label', 'roi', 'label_info', 'selected_label_name', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path']
WARNING: In C:\P\IPP\ITK-source\ITK\Modules\IO\GDCM\src\itkGDCMSeriesFileNames.cxx, line 100
GDCMSeriesFileNames (0000028C7EB57BE0): No Series were found

[2023-08-18 20:26:18,255] [26416] [MainThread] [ERROR] (uvicorn.error:434) - Exception in ASGI application
Traceback (most recent call last):
  File "C:\Program Files\Python38\lib\site-packages\uvicorn\protocols\http\h11_impl.py", line 429, in run_asgi
    result = await app(  # type: ignore[func-returns-value]
  File "C:\Program Files\Python38\lib\site-packages\uvicorn\middleware\proxy_headers.py", line 78, in __call__
    return await self.app(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\fastapi\applications.py", line 276, in __call__
    await super().__call__(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\applications.py", line 122, in __call__
    await self.middleware_stack(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\middleware\errors.py", line 184, in __call__
    raise exc
  File "C:\Program Files\Python38\lib\site-packages\starlette\middleware\errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\middleware\cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\middleware\exceptions.py", line 79, in __call__
    raise exc
  File "C:\Program Files\Python38\lib\site-packages\starlette\middleware\exceptions.py", line 68, in __call__
    await self.app(scope, receive, sender)
  File "C:\Program Files\Python38\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 21, in __call__
    raise e
  File "C:\Program Files\Python38\lib\site-packages\fastapi\middleware\asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 718, in __call__
    await route.handle(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 276, in handle
    await self.app(scope, receive, send)
  File "C:\Program Files\Python38\lib\site-packages\starlette\routing.py", line 66, in app
    response = await func(request)
  File "C:\Program Files\Python38\lib\site-packages\fastapi\routing.py", line 237, in app
    raw_response = await run_endpoint_function(
  File "C:\Program Files\Python38\lib\site-packages\fastapi\routing.py", line 163, in run_endpoint_function
    return await dependant.call(**values)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\endpoints\infer.py", line 180, in api_run_inference
    return run_inference(background_tasks, model, image, session_id, params, file, label, output)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\endpoints\infer.py", line 162, in run_inference
    result = instance.infer(request)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\app.py", line 307, in infer
    result_file_name, result_json = task(request)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\infer\basic_infer.py", line 295, in __call__
    data = self.run_pre_transforms(data, pre_transforms)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\tasks\infer\basic_infer.py", line 386, in run_pre_transforms
    return run_transforms(data, transforms, log_prefix="PRE", use_compose=False)
  File "C:\Program Files\Python38\lib\site-packages\monailabel\interfaces\utils\transform.py", line 106, in run_transforms
    data = t(data)
  File "C:\Program Files\Python38\lib\site-packages\monai\transforms\io\dictionary.py", line 164, in __call__
    data = self._loader(d[key], reader)
  File "C:\Program Files\Python38\lib\site-packages\monai\transforms\io\array.py", line 263, in __call__
    img = reader.read(filename)
  File "C:\Program Files\Python38\lib\site-packages\monai\data\image_reader.py", line 241, in read
    raise FileNotFoundError(f"no DICOMs in: {name}.")
FileNotFoundError: no DICOMs in: ..

diazandr3s Aug 19, 2023
Maintainer

Hi @VSPuzzler,

It seems you don't have annotated samples to train the model. This is what I'm seeing from the logs:

ValueError: num_samples should be a positive integer value, but got num_samples=0

Did you organize the volumes as shown here or here? Are you using NIfTI or DICOM format?

If using DICOM format, you have to use a DICOM Web server. Otherwise, images have to be converted to NIfTI.

Hope this helps,

Answer selected by VSPuzzler

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MONAILabel server not responding and given this error: [25188] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting. #1526

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MONAILabel server not responding and given this error: [25188] [MainThread] [ERROR] (uvicorn.error:59) - Application startup failed. Exiting. #1526

VSPuzzler Aug 17, 2023

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tangy5 Aug 17, 2023 Maintainer

VSPuzzler Aug 18, 2023 Author

diazandr3s Aug 18, 2023 Maintainer

VSPuzzler Aug 19, 2023 Author

diazandr3s Aug 19, 2023 Maintainer

VSPuzzler
Aug 17, 2023

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tangy5
Aug 17, 2023
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VSPuzzler Aug 18, 2023
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diazandr3s Aug 18, 2023
Maintainer

VSPuzzler Aug 19, 2023
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diazandr3s Aug 19, 2023
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