Failed to run inference in MONAI Label Server

Support
1

Hello,

We are trying to use MONAI Label to train an AI on our own dataset.
I have installed MONAI Label following the instructions in GitHub, but I get the;

Traceback (most recent call last):
  File "C:/Users/WS000039/AppData/Local/NA-MIC/Slicer 4.13.0-2021-09-13/NA-MIC/Extensions-30181/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 1532, in onClickSegmentation
    result_file, params = self.logic.infer(model, image_file, self.getParamsFromConfig("infer", model))
  File "C:/Users/WS000039/AppData/Local/NA-MIC/Slicer 4.13.0-2021-09-13/NA-MIC/Extensions-30181/MONAILabel/lib/Slicer-4.13/qt-scripted-modules/MONAILabel.py", line 1815, in infer
    result_file, params = client.infer(model, image_in, params, label_in)
  File "C:\Users\WS000039\AppData\Local\NA-MIC\Slicer 4.13.0-2021-09-13\NA-MIC\Extensions-30181\MONAILabel\lib\Slicer-4.13\qt-scripted-modules\MONAILabelLib\client.py", line 111, in infer
    "Status: {}; Response: {}".format(status, form),
MONAILabelLib.client.MONAILabelException: (2, "Status: 500; Response: b'Internal Server Error'")

Even when running one of the spleen example datasets

error
error1920×1040 214 KB

1 Like
2

Hi @Fluvio_Lobo,

Can you please also add the server logs? You can get them from https://127.0.0.1:8000/logs or in the folder App (deepedit/logs).

Thanks!

Andres

3

@diazandr3s,

Sorry for the delay, I had to set-up MONAI-Label in my home computer.
I do get the same issue and here is the logfile;

[2021-12-05 21:39:03,625] [25408] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:39:14,539] [24708] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:40:22,041] [17392] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:41:40,682] [24228] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:43:03,432] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:43:03,483] [8820] [MainThread] [INFO] (monailabel.utils.others.class_utils:35) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2021-12-05 21:43:04,219] [8820] [MainThread] [INFO] (main:104) - Pretrained Model Path: https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:43:04,220] [8820] [MainThread] [INFO] (monailabel.interfaces.app:527) - Downloading resource: C:\Users\WOLF512\apps\deepedit\model\pretrained_dynunet.pt from https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:43:34,967] [8820] [MainThread] [INFO] (main:109) - EPISTEMIC Enabled: 0; Samples: 5
[2021-12-05 21:43:34,968] [8820] [MainThread] [INFO] (main:113) - TTA Enabled: 0; Samples: 5
[2021-12-05 21:43:34,971] [8820] [MainThread] [INFO] (monailabel.interfaces.app:115) - Init Datastore for: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr
[2021-12-05 21:43:34,973] [8820] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd']
[2021-12-05 21:43:34,989] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_10 => spleen_10.nii.gz
[2021-12-05 21:43:35,086] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_12 => spleen_12.nii.gz
[2021-12-05 21:43:35,217] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_13 => spleen_13.nii.gz
[2021-12-05 21:43:35,287] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_14 => spleen_14.nii.gz
[2021-12-05 21:43:35,337] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_16 => spleen_16.nii.gz
[2021-12-05 21:43:35,402] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_17 => spleen_17.nii.gz
[2021-12-05 21:43:35,482] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_18 => spleen_18.nii.gz
[2021-12-05 21:43:35,606] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_19 => spleen_19.nii.gz
[2021-12-05 21:43:35,655] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_2 => spleen_2.nii.gz
[2021-12-05 21:43:35,735] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_20 => spleen_20.nii.gz
[2021-12-05 21:43:35,858] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_21 => spleen_21.nii.gz
[2021-12-05 21:43:35,932] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_22 => spleen_22.nii.gz
[2021-12-05 21:43:36,049] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_24 => spleen_24.nii.gz
[2021-12-05 21:43:36,145] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_25 => spleen_25.nii.gz
[2021-12-05 21:43:36,222] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_26 => spleen_26.nii.gz
[2021-12-05 21:43:36,281] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_27 => spleen_27.nii.gz
[2021-12-05 21:43:36,391] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_28 => spleen_28.nii.gz
[2021-12-05 21:43:36,433] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_29 => spleen_29.nii.gz
[2021-12-05 21:43:36,520] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_3 => spleen_3.nii.gz
[2021-12-05 21:43:36,560] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_31 => spleen_31.nii.gz
[2021-12-05 21:43:36,620] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_32 => spleen_32.nii.gz
[2021-12-05 21:43:36,715] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_33 => spleen_33.nii.gz
[2021-12-05 21:43:36,785] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_38 => spleen_38.nii.gz
[2021-12-05 21:43:36,870] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_40 => spleen_40.nii.gz
[2021-12-05 21:43:36,960] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_41 => spleen_41.nii.gz
[2021-12-05 21:43:37,049] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_44 => spleen_44.nii.gz
[2021-12-05 21:43:37,122] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_45 => spleen_45.nii.gz
[2021-12-05 21:43:37,212] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_46 => spleen_46.nii.gz
[2021-12-05 21:43:37,300] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_47 => spleen_47.nii.gz
[2021-12-05 21:43:37,390] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_49 => spleen_49.nii.gz
[2021-12-05 21:43:37,457] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_52 => spleen_52.nii.gz
[2021-12-05 21:43:37,582] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_53 => spleen_53.nii.gz
[2021-12-05 21:43:37,742] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_56 => spleen_56.nii.gz
[2021-12-05 21:43:37,776] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_59 => spleen_59.nii.gz
[2021-12-05 21:43:37,824] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_6 => spleen_6.nii.gz
[2021-12-05 21:43:37,945] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_60 => spleen_60.nii.gz
[2021-12-05 21:43:38,042] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_61 => spleen_61.nii.gz
[2021-12-05 21:43:38,130] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_62 => spleen_62.nii.gz
[2021-12-05 21:43:38,201] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_63 => spleen_63.nii.gz
[2021-12-05 21:43:38,260] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_8 => spleen_8.nii.gz
[2021-12-05 21:43:38,295] [8820] [MainThread] [INFO] (monailabel.datastore.local:551) - Adding New Image: spleen_9 => spleen_9.nii.gz
[2021-12-05 21:43:38,344] [8820] [MainThread] [INFO] (monailabel.datastore.local:534) - Invalidate count: 41
[2021-12-05 21:43:38,347] [8820] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2021-12-05 21:43:40,676] [8820] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\WOLF512\.cache\monailabel\sessions
[2021-12-05 21:43:40,676] [8820] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2021-12-05 21:43:40,678] [8820] [MainThread] [INFO] (monailabel.interfaces.app:396) - App Init - completed
[2021-12-05 21:43:40,679] [8820] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Scoring request: {'method': 'dice'}
[2021-12-05 21:43:40,680] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:57) - COMMAND:: C:\Users\WOLF512\AppData\Local\Programs\Python\Python39\python.exe -m monailabel.interfaces.utils.app -m scoring -r {"method":"dice","gpus":"all"}
[2021-12-05 21:43:40,681] [8820] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Scoring request: {'method': 'sum'}
[2021-12-05 21:43:40,681] [8820] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2021-12-05 21:43:40,682] [8820] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x000002318F0A3D30>
[2021-12-05 21:43:40,683] [8820] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2021-12-05 21:43:40,883] [4956] [MainThread] [INFO] (__main__:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:43:43,699] [4956] [MainThread] [INFO] (monailabel.utils.others.class_utils:35) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2021-12-05 21:43:44,601] [4956] [MainThread] [INFO] (main:104) - Pretrained Model Path: https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:43:44,602] [4956] [MainThread] [INFO] (main:109) - EPISTEMIC Enabled: 0; Samples: 5
[2021-12-05 21:43:44,602] [4956] [MainThread] [INFO] (main:113) - TTA Enabled: 0; Samples: 5
[2021-12-05 21:43:44,602] [4956] [MainThread] [INFO] (monailabel.interfaces.app:115) - Init Datastore for: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr
[2021-12-05 21:43:44,602] [4956] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd']
[2021-12-05 21:43:44,633] [4956] [MainThread] [INFO] (monailabel.datastore.local:534) - Invalidate count: 0
[2021-12-05 21:43:44,633] [4956] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2021-12-05 21:43:44,665] [4956] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\WOLF512\.cache\monailabel\sessions
[2021-12-05 21:43:44,665] [4956] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2021-12-05 21:43:44,666] [4956] [MainThread] [INFO] (__main__:62) - Result: {}
[2021-12-05 21:43:45,227] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:75) - Return code: 0
[2021-12-05 21:43:45,229] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:57) - COMMAND:: C:\Users\WOLF512\AppData\Local\Programs\Python\Python39\python.exe -m monailabel.interfaces.utils.app -m scoring -r {"method":"sum","gpus":"all"}
[2021-12-05 21:43:45,426] [4628] [MainThread] [INFO] (__main__:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:43:48,267] [4628] [MainThread] [INFO] (monailabel.utils.others.class_utils:35) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2021-12-05 21:43:49,008] [4628] [MainThread] [INFO] (main:104) - Pretrained Model Path: https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:43:49,008] [4628] [MainThread] [INFO] (main:109) - EPISTEMIC Enabled: 0; Samples: 5
[2021-12-05 21:43:49,009] [4628] [MainThread] [INFO] (main:113) - TTA Enabled: 0; Samples: 5
[2021-12-05 21:43:49,009] [4628] [MainThread] [INFO] (monailabel.interfaces.app:115) - Init Datastore for: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr
[2021-12-05 21:43:49,009] [4628] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd']
[2021-12-05 21:43:49,030] [4628] [MainThread] [INFO] (monailabel.datastore.local:534) - Invalidate count: 0
[2021-12-05 21:43:49,030] [4628] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2021-12-05 21:43:49,059] [4628] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\WOLF512\.cache\monailabel\sessions
[2021-12-05 21:43:49,059] [4628] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2021-12-05 21:43:49,060] [4628] [MainThread] [INFO] (__main__:62) - Result: {}
[2021-12-05 21:43:49,535] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:75) - Return code: 0
[2021-12-05 21:43:57,697] [8820] [MainThread] [INFO] (monailabel.endpoints.activelearning:42) - Active Learning Request: {'strategy': 'random'}
[2021-12-05 21:43:57,706] [8820] [MainThread] [INFO] (monailabel.tasks.activelearning.random:44) - Random: Images: ['spleen_10', 'spleen_12', 'spleen_13', 'spleen_14', 'spleen_16', 'spleen_17', 'spleen_18', 'spleen_19', 'spleen_2', 'spleen_20', 'spleen_21', 'spleen_22', 'spleen_24', 'spleen_25', 'spleen_26', 'spleen_27', 'spleen_28', 'spleen_29', 'spleen_3', 'spleen_31', 'spleen_32', 'spleen_33', 'spleen_38', 'spleen_40', 'spleen_41', 'spleen_44', 'spleen_45', 'spleen_46', 'spleen_47', 'spleen_49', 'spleen_52', 'spleen_53', 'spleen_56', 'spleen_59', 'spleen_6', 'spleen_60', 'spleen_61', 'spleen_62', 'spleen_63', 'spleen_8', 'spleen_9']; Weight: [1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637, 1638758637]
[2021-12-05 21:43:57,706] [8820] [MainThread] [INFO] (monailabel.tasks.activelearning.random:45) - Random: Selected Image: spleen_52
[2021-12-05 21:43:57,707] [8820] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Scoring request: {'method': 'dice'}
[2021-12-05 21:43:57,708] [8820] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Scoring request: {'method': 'sum'}
[2021-12-05 21:43:57,709] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:57) - COMMAND:: C:\Users\WOLF512\AppData\Local\Programs\Python\Python39\python.exe -m monailabel.interfaces.utils.app -m scoring -r {"method":"dice","gpus":"all"}
[2021-12-05 21:43:57,715] [8820] [MainThread] [INFO] (monailabel.endpoints.activelearning:58) - Next sample: {'id': 'spleen_52', 'ts': 1638758617, 'checksum': 'SHA256:689d690d0fc10324c2a5ef3b0c883d07a9412619f69e0475b0b8cbabb75fd5cb', 'name': 'spleen_52.nii.gz', 'path': 'C:\\Users\\WOLF512\\datasets\\Task09_Spleen\\imagesTr\\spleen_52.nii.gz'}
[2021-12-05 21:43:57,882] [22940] [MainThread] [INFO] (__main__:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:43:59,150] [8820] [MainThread] [INFO] (monailabel.endpoints.infer:147) - Infer Request: {'model': 'deepedit_seg', 'image': 'spleen_52'}
[2021-12-05 21:43:59,152] [8820] [MainThread] [INFO] (monailabel.interfaces.app:224) - Image => C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr\spleen_52.nii.gz
[2021-12-05 21:43:59,152] [8820] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:218) - Infer Request (final): {'model': 'deepedit_seg', 'image': 'C:\\Users\\WOLF512\\datasets\\Task09_Spleen\\imagesTr\\spleen_52.nii.gz'}
[2021-12-05 21:43:59,155] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:61) - PRE - Run Transform
[2021-12-05 21:43:59,155] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:62) - PRE - Input Keys: dict_keys(['model', 'image', 'image_path'])
[2021-12-05 21:43:59,965] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (LoadImaged): Time: 0.8081; image: (512, 512, 112)(float32)
[2021-12-05 21:43:59,966] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (SingleLabelSingleModalityd): Time: 0.0000; image: (512, 512, 112)(float32)
[2021-12-05 21:43:59,967] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (AddChanneld): Time: 0.0000; image: (1, 512, 512, 112)(float32)
[2021-12-05 21:44:02,089] [22940] [MainThread] [INFO] (monailabel.utils.others.class_utils:35) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2021-12-05 21:44:04,430] [22940] [MainThread] [INFO] (main:104) - Pretrained Model Path: https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:44:04,430] [22940] [MainThread] [INFO] (main:109) - EPISTEMIC Enabled: 0; Samples: 5
[2021-12-05 21:44:04,430] [22940] [MainThread] [INFO] (main:113) - TTA Enabled: 0; Samples: 5
[2021-12-05 21:44:04,430] [22940] [MainThread] [INFO] (monailabel.interfaces.app:115) - Init Datastore for: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr
[2021-12-05 21:44:04,431] [22940] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd']
[2021-12-05 21:44:04,470] [22940] [MainThread] [INFO] (monailabel.datastore.local:534) - Invalidate count: 0
[2021-12-05 21:44:04,470] [22940] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2021-12-05 21:44:04,503] [22940] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\WOLF512\.cache\monailabel\sessions
[2021-12-05 21:44:04,503] [22940] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2021-12-05 21:44:04,503] [22940] [MainThread] [INFO] (__main__:62) - Result: {}
[2021-12-05 21:44:05,158] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:75) - Return code: 0
[2021-12-05 21:44:05,159] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:57) - COMMAND:: C:\Users\WOLF512\AppData\Local\Programs\Python\Python39\python.exe -m monailabel.interfaces.utils.app -m scoring -r {"method":"sum","gpus":"all"}
[2021-12-05 21:44:05,336] [24840] [MainThread] [INFO] (__main__:38) - Initializing App from: C:\Users\WOLF512\apps\deepedit; studies: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr; conf: {}
[2021-12-05 21:44:08,168] [24840] [MainThread] [INFO] (monailabel.utils.others.class_utils:35) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2021-12-05 21:44:08,800] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (Spacingd): Time: 8.8329; image: (1, 412, 412, 445)(float32)
[2021-12-05 21:44:08,802] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (Orientationd): Time: 0.0020; image: (1, 412, 412, 445)(float32)
[2021-12-05 21:44:09,212] [24840] [MainThread] [INFO] (main:104) - Pretrained Model Path: https://github.com/Project-MONAI/MONAILabel/releases/download/data/deepedit_dynunet_spleen.pt
[2021-12-05 21:44:09,212] [24840] [MainThread] [INFO] (main:109) - EPISTEMIC Enabled: 0; Samples: 5
[2021-12-05 21:44:09,213] [24840] [MainThread] [INFO] (main:113) - TTA Enabled: 0; Samples: 5
[2021-12-05 21:44:09,213] [24840] [MainThread] [INFO] (monailabel.interfaces.app:115) - Init Datastore for: C:\Users\WOLF512\datasets\Task09_Spleen\imagesTr
[2021-12-05 21:44:09,213] [24840] [MainThread] [INFO] (monailabel.datastore.local:125) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd']
[2021-12-05 21:44:09,236] [24840] [MainThread] [INFO] (monailabel.datastore.local:534) - Invalidate count: 0
[2021-12-05 21:44:09,236] [24840] [MainThread] [INFO] (monailabel.datastore.local:145) - Start observing external modifications on datastore (AUTO RELOAD)
[2021-12-05 21:44:09,265] [24840] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\WOLF512\.cache\monailabel\sessions
[2021-12-05 21:44:09,265] [24840] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2021-12-05 21:44:09,266] [24840] [MainThread] [INFO] (__main__:62) - Result: {}
[2021-12-05 21:44:09,929] [8820] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:75) - Return code: 0
[2021-12-05 21:44:10,948] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (NormalizeIntensityd): Time: 2.1451; image: (1, 412, 412, 445)(float32)
[2021-12-05 21:44:11,347] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (Resized): Time: 0.3982; image: (1, 256, 256, 128)(float32)
[2021-12-05 21:44:11,432] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (DiscardAddGuidanced): Time: 0.0828; image: (3, 256, 256, 128)(float32)
[2021-12-05 21:44:11,432] [8820] [MainThread] [INFO] (monailabel.interfaces.utils.transform:98) - PRE - Transform (ToTensord): Time: 0.0000; image: torch.Size([3, 256, 256, 128])(torch.float32)
[2021-12-05 21:44:11,433] [8820] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:341) - Running Inferer:: SimpleInferer
[2021-12-05 21:44:11,433] [8820] [MainThread] [INFO] (monailabel.interfaces.tasks.infer:294) - Infer model path: C:\Users\WOLF512\apps\deepedit\model\pretrained_dynunet.pt
1 Like
4

@diazandr3s,

Quick Update!
While the log does not show it, the terminal had a message saying something in line with running as a CPU system only

I looked over the installation prerequisites and saw that I missed the actual installation of Pytorch with CUDA.

Now I get this however;

RuntimeError: CUDA out of memory. Tried to allocate 1024.00 MiB (GPU 0; 4.00 GiB total capacity; 2.21 GiB already allocated; 481.27 MiB free; 2.25 GiB reserved in total by PyTorch)
1 Like
5

Thanks for the update, @Fluvio_Lobo
Can you please run in a terminal the nvidia-smi command to check which GPU card and memory is available on your PC?
By default, the DeepEdit App uses 256x256x128 as the image size to train and do inference (MONAILabel/main.py at main · Project-MONAI/MONAILabel · GitHub). I think the available GPU is not enough for this image size. My recommendation is to train a model using an image size of 128x128x128 or another that fits in the available GPU memory.

Please let me know,

6

@diazandr3s,

I will test this at work today. I think this is a reminder that I need an upgrade at home :sweat_smile:

I do have more questions regarding these limits;

  • What is the relationship between image dimensions (or overall number of voxels) and memory size required?

  • main.py also has a line for “target spacing”…these are just default values that get updated with the new image, correct? The image size is still the limiting factor

   spatial_size = json.loads(conf.get("spatial_size", "[256, 256, 128]"))
   target_spacing = json.loads(conf.get("target_spacing", "[1.0, 1.0, 1.0]"))

Thank you!

1 Like
7

@Fluvio_Lobo,

What is the relationship between image dimensions (or overall number of voxels) and memory size required?

This is not easy to tell as it also depends on the network hyperparameters and the transformations (data augmentation) you apply to the images. For instance, you can check here (https://tinyurl.com/tableGPUMemory) an empirical relation between image size and the DynUNet (MONAILabel/main.py at main · Project-MONAI/MONAILabel · GitHub).

main.py also has a line for “target spacing”…these are just default values that get updated with the new image, correct? The image size is still the limiting factor

“Target spacing” is the spatial resolution we use to train and do inference. This is the default value and it does not change once you start the training process.
For understanding purposes, you may want to check how the spatial resolution varies among the dataset. Otherwise, you can think of this as a sort of normalization.

Best,

1 Like
8

@diazandr3s,

Thanks for the clarification!

main.py also has a line for “target spacing”…these are just default values that get updated with the new image, correct? The image size is still the limiting factor

“Target spacing” is the spatial resolution we use to train and do inference. This is the default value and it does not change once you start the training process.
For understanding purposes, you may want to check how the spatial resolution varies among the dataset. Otherwise, you can think of this as a sort of normalization.

If we had a dataset with a spatial resolution below 1.00 mm. Or, perhaps, we resample the data to below 1.00 mm, do we then update this value before running the training?

1 Like
9

That’s right. This is the argument you should update with the desired spatial resolution before training.