Describe the bug When using a fairly straightforward non-interactive segmentation model, I expected to be able to provide a handful of manual segmentations, train the model, and simply run the auto segmentation to finish up the rest of my dataset.

However, I unfortunately can't select the model in the Auto Segmentation header.

I am using a custom implementation of the segmentation_spleen.py example files, with only the label name and class names changed.

To Reproduce Steps to reproduce the behavior:

1. Provide a number of manual segmentations to start off the segmentation model
2. Train model successfully
3. Notice that there is no way to actually use the trained model

Expected behavior After providing a few manual segmentations, I expect to be able to use the now trained model in segmenting my anatomy of choice.

Screenshots

Environment

Ensuring you use the relevant python executable, please paste the output of:

================================
Printing MONAI config...
================================
MONAI version: 0.9.0
Numpy version: 1.22.4
Pytorch version: 1.11.0+cpu
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: af0e0e9f757558d144b655c63afcea3a4e0a06f5
MONAI __file__: C:\Users\[Username]\AppData\Local\pypoetry\Cache\virtualenvs\nnunetdocker-uHdzYLSm-py3.9\lib\site-packages\monai\__init__.py

Optional dependencies:
Pytorch Ignite version: 0.4.8
Nibabel version: 3.2.2
scikit-image version: 0.19.3
Pillow version: 9.1.1
Tensorboard version: 2.9.1
gdown version: 4.4.0
TorchVision version: 0.12.0+cpu
tqdm version: 4.64.0
lmdb version: 1.3.0
psutil version: 5.9.1
pandas version: 1.4.2
einops version: 0.4.1
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: 0.4.3

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Windows
Win32 version: ('10', '10.0.19044', 'SP0', 'Multiprocessor Free')
Win32 edition: Enterprise
Platform: Windows-10-10.0.19044-SP0
Processor: Intel64 Family 6 Model 85 Stepping 4, GenuineIntel
Machine: AMD64
Python version: 3.9.13
Process name: python.exe
Command: ['C:\\Users\\[Username]\\AppData\\Local\\Programs\\Python\\Python39\\python.exe', '-c', 'import monai; monai.config.print_debug_info()']
Open files: [popenfile(path='C:\\Windows\\System32\\en-US\\kernel32.dll.mui', fd=-1), popenfile(path='C:\\Windows\\System32\\en-US\\tzres.dll.mui', fd=-1), popenfile(path='C:\\Windows\\System32\\en-US\\KernelBase.dll.mui', fd=-1)]  
Num physical CPUs: 12
Num logical CPUs: 24
Num usable CPUs: 24
CPU usage (%): [5.0, 3.8, 1.9, 0.6, 0.0, 1.2, 1.9, 1.9, 0.6, 0.0, 0.6, 0.6, 2.5, 72.3, 0.6, 0.6, 0.6, 1.2, 1.9, 0.0, 1.2, 1.9, 0.0, 13.8]
CPU freq. (MHz): 3504
Load avg. in last 1, 5, 15 mins (%): [0.0, 0.0, 0.0]
Disk usage (%): 66.6
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 31.7
Available memory (GB): 15.7
Used memory (GB): 16.0

================================
Printing GPU config...
================================
Num GPUs: 0
Has CUDA: False
cuDNN enabled: False

Additional context None, however CUDA 11.6 and 11.7 are installed, and nvidia-smi works, while MONAI tells me CUDA is not available. This is (probably) not relevant to my issue though, and I might open a new issue for that.

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?

Describe the bug I am trying to use OHIF viewer. When trying to run monailabel start_server --app apps\deepedit --studies http://127.0.0.1:8042/dicom-web this URL , it pops up with a dialogbox to enter the username and password.

I tried some default username and password, but it doesn't signed into the Orthanc Server.

To Reproduce Steps to reproduce the behavior: For this, I followed the below steps which was mentioned in the document.

1. Installed Orthanc using apt-get install orthanc orthanc-dicomweb.
2. Upgraded to latest version by following steps mentioned here

Now the orthanc server setup is completed.

1. Run the command monailabel start_server --app apps\deepedit --studies http://127.0.0.1:8042/dicom-web

Expected behavior

I expect that orthanc server should load without the authentication pop up.

Screenshots

Environment

================================
Printing MONAI config...
================================
MONAI version: 0.9.dev2149
Numpy version: 1.21.4
Pytorch version: 1.9.0+cu111
MONAI flags: HAS_EXT = False, USE_COMPILED = False
MONAI rev id: 1ad68787c35e259cb7704b56d679659104d2494c

Optional dependencies:
Pytorch Ignite version: 0.4.6
Nibabel version: 3.2.1
scikit-image version: 0.18.3
Pillow version: 8.4.0
Tensorboard version: 2.7.0
gdown version: 4.2.0
TorchVision version: 0.10.0+cu111
tqdm version: 4.62.3
lmdb version: 1.2.1
psutil version: 5.8.0
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: NOT INSTALLED or UNKNOWN VERSION.
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Linux
Linux version: Ubuntu 20.04.3 LTS
Platform: Linux-4.15.0-136-generic-x86_64-with-glibc2.10
Processor: x86_64
Machine: x86_64
Python version: 3.8.10
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: []
Num physical CPUs: 20
Num logical CPUs: 40
Num usable CPUs: 40
CPU usage (%): [10.3, 11.3, 11.3, 11.9, 9.5, 11.8, 100.0, 9.4, 12.6, 8.9, 11.3, 10.7, 10.1, 13.3, 13.2, 10.2, 10.7, 16.9, 9.6, 9.5, 11.5, 10.1, 11.3, 9.5, 11.9, 8.9, 9.4, 10.1, 16.9, 11.9, 9.5, 10.1, 10.7, 10.1, 10.1, 10.1, 10.7, 10.1, 10.3, 14.6]
CPU freq. (MHz): 1461
Load avg. in last 1, 5, 15 mins (%): [1.7, 2.8, 4.1]
Disk usage (%): 73.7
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 251.8
Available memory (GB): 237.8
Used memory (GB): 12.8

================================
Printing GPU config...
================================
Num GPUs: 4
Has CUDA: True
CUDA version: 11.1
cuDNN enabled: True
cuDNN version: 8005
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_70', 'sm_75', 'sm_80', 'sm_86']
GPU 0 Name: Tesla V100-DGXS-32GB
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 80
GPU 0 Total memory (GB): 31.7
GPU 0 CUDA capability (maj.min): 7.0
GPU 1 Name: Tesla V100-DGXS-32GB
GPU 1 Is integrated: False
GPU 1 Is multi GPU board: False
GPU 1 Multi processor count: 80
GPU 1 Total memory (GB): 31.7
GPU 1 CUDA capability (maj.min): 7.0
GPU 2 Name: Tesla V100-DGXS-32GB
GPU 2 Is integrated: False
GPU 2 Is multi GPU board: False
GPU 2 Multi processor count: 80
GPU 2 Total memory (GB): 31.7
GPU 2 CUDA capability (maj.min): 7.0
GPU 3 Name: Tesla V100-DGXS-32GB
GPU 3 Is integrated: False
GPU 3 Is multi GPU board: False
GPU 3 Multi processor count: 80
GPU 3 Total memory (GB): 31.7
GPU 3 CUDA capability (maj.min): 7.0

Additional context I installed the orthanc in DGX docker container.

Any suggestion and help is appreciated. Thank you

Describe the bug

When I use the Next Sample button, the retrieved displayed volume name is incorrect. That's because i believe parser incorrectly cuts at the volume name at "-" sign of the volume. Below is the log from the python interactor, displaying the correct volume name. In slicer, regardless of the volume, all retrieved volumes are displayed as 15.5_baseline in Slicer, which confuses the user.

Check if file exists/shared locally: /workspace/undeterminedSex_AAMN_N305-17-e15.5_baseline.nii.gz => False
http://127.0.0.1:8000/datastore/image?image=undeterminedSex_AAMN_N305-17-e15.5_baseline

Is your feature request related to a problem? Please describe. MONAILabel V1 only supports server-sided hosting of data.

For clinical use, we want our research assistants to be able to use MONAILabel from individual computers. A workstation with a dedicated GPU was assigned to be the remote-server, receiving client requests for annotating data and returning the annotation to the client.

Describe the solution you'd like Clients should be able to send images for automatic annotation to the MONAILabel server.

Additional context https://github.com/JolleyLabCHOP/DeepHeart/issues/1 https://github.com/JolleyLabCHOP/DeepHeart/issues/2

Dear Experts,

Greetings from Mumbai, India.

At the outset thank you for the open source application for image annotation and segmentation.

I attempted segmentation model training on monailabel server deployed on WSL, however, training failed. Please find the entire log below for perusal and inputs:

monailabel start_server --app apps/radiology --studies /mnt/h/Cases/TMH/Liver/ --conf models segmentation --host 0.0.0.0 --port 8080
Using PYTHONPATH=/home/amitjc:

Failed to load image Python extension: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory
2022-09-25 04:23:11,658 - USING:: version = False
2022-09-25 04:23:11,658 - USING:: app = /home/amitjc/apps/radiology
2022-09-25 04:23:11,658 - USING:: studies = /mnt/h/Cases/TMH/Liver
2022-09-25 04:23:11,658 - USING:: verbose = INFO
2022-09-25 04:23:11,658 - USING:: conf = [['models', 'segmentation']]
2022-09-25 04:23:11,658 - USING:: host = 0.0.0.0
2022-09-25 04:23:11,658 - USING:: port = 8080
2022-09-25 04:23:11,658 - USING:: uvicorn_app = monailabel.app:app
2022-09-25 04:23:11,658 - USING:: ssl_keyfile = None
2022-09-25 04:23:11,658 - USING:: ssl_certfile = None
2022-09-25 04:23:11,658 - USING:: ssl_keyfile_password = None
2022-09-25 04:23:11,658 - USING:: ssl_ca_certs = None
2022-09-25 04:23:11,658 - USING:: workers = None
2022-09-25 04:23:11,658 - USING:: limit_concurrency = None
2022-09-25 04:23:11,658 - USING:: access_log = False
2022-09-25 04:23:11,658 - USING:: log_config = None
2022-09-25 04:23:11,658 - USING:: dryrun = False
2022-09-25 04:23:11,658 - USING:: action = start_server
2022-09-25 04:23:11,658 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2022-09-25 04:23:11,658 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2022-09-25 04:23:11,658 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2022-09-25 04:23:11,658 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2022-09-25 04:23:11,659 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2022-09-25 04:23:11,660 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2022-09-25 04:23:11,660 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2022-09-25 04:23:11,660 -
Allow Origins: ['*']
[2022-09-25 04:23:12,084] [393] [MainThread] [INFO] (uvicorn.error:75) - Started server process [393]
[2022-09-25 04:23:12,084] [393] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2022-09-25 04:23:12,084] [393] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/amitjc/apps/radiology; studies: /mnt/h/Cases/TMH/Liver; conf: {'models': 'segmentation'}
[2022-09-25 04:23:12,354] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-09-25 04:23:12,361] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2022-09-25 04:23:12,361] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2022-09-25 04:23:12,362] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2022-09-25 04:23:12,362] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2022-09-25 04:23:12,366] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2022-09-25 04:23:12,366] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2022-09-25 04:23:12,367] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2022-09-25 04:23:12,367] [393] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2022-09-25 04:23:12,367] [393] [MainThread] [INFO] (main:86) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2022-09-25 04:23:12,406] [393] [MainThread] [INFO] (main:90) - +++ Using Models: ['segmentation']
[2022-09-25 04:23:12,406] [393] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /mnt/h/Cases/TMH/Liver
[2022-09-25 04:23:12,406] [393] [MainThread] [INFO] (monailabel.datastore.local:126) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2022-09-25 04:23:12,474] [393] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-09-25 04:23:12,474] [393] [MainThread] [INFO] (monailabel.datastore.local:146) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-09-25 04:23:12,602] [393] [MainThread] [INFO] (main:116) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x7f413c5adeb0>
[2022-09-25 04:23:12,602] [393] [MainThread] [INFO] (main:172) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x7f413c5adeb0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7f4134049850>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7f4134049880>}
[2022-09-25 04:23:12,602] [393] [MainThread] [INFO] (main:185) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x7f4133ff67c0>
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/amitjc/.cache/monailabel/sessions
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (monailabel.interfaces.app:465) - App Init - completed
[2022-09-25 04:23:12,603] [timeloop] [INFO] Starting Timeloop..
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2022-09-25 04:23:12,603] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f4133fff160>
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f4133fff160>
[2022-09-25 04:23:12,603] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2022-09-25 04:23:12,603] [393] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8080 (Press CTRL+C to quit)
[2022-09-25 04:31:28,445] [393] [MainThread] [INFO] (monailabel.endpoints.datastore:67) - Image: CV17056; File: <starlette.datastructures.UploadFile object at 0x7f414e2283d0>; params: {"client_id": "user-xyz"}
[2022-09-25 04:31:28,513] [393] [MainThread] [INFO] (monailabel.datastore.local:402) - Adding Image: CV17056 => /tmp/tmpyt7z7vu_.nii.gz
[2022-09-25 04:36:30,193] [393] [MainThread] [INFO] (monailabel.endpoints.datastore:100) - Saving Label for CV17056 for tag: final by admin
[2022-09-25 04:36:30,194] [393] [MainThread] [INFO] (monailabel.endpoints.datastore:111) - Save Label params: {"label_info": [{"name": "spleen", "idx": 1}, {"name": "right kidney", "idx": 2}, {"name": "left kidney", "idx": 3}, {"name": "gallbladder", "idx": 4}, {"name": "esophagus", "idx": 5}, {"name": "liver", "idx": 6}, {"name": "stomach", "idx": 7}, {"name": "aorta", "idx": 8}, {"name": "inferior vena cava", "idx": 9}, {"name": "portal vein and splenic vein", "idx": 10}, {"name": "pancreas", "idx": 11}, {"name": "right adrenal gland", "idx": 12}, {"name": "left adrenal gland", "idx": 13}], "client_id": "user-xyz"}
[2022-09-25 04:36:30,194] [393] [MainThread] [INFO] (monailabel.datastore.local:449) - Saving Label for Image: CV17056; Tag: final; Info: {'label_info': [{'name': 'spleen', 'idx': 1}, {'name': 'right kidney', 'idx': 2}, {'name': 'left kidney', 'idx': 3}, {'name': 'gallbladder', 'idx': 4}, {'name': 'esophagus', 'idx': 5}, {'name': 'liver', 'idx': 6}, {'name': 'stomach', 'idx': 7}, {'name': 'aorta', 'idx': 8}, {'name': 'inferior vena cava', 'idx': 9}, {'name': 'portal vein and splenic vein', 'idx': 10}, {'name': 'pancreas', 'idx': 11}, {'name': 'right adrenal gland', 'idx': 12}, {'name': 'left adrenal gland', 'idx': 13}], 'client_id': 'user-xyz'}
[2022-09-25 04:36:30,194] [393] [MainThread] [INFO] (monailabel.datastore.local:457) - Adding Label: CV17056 => final => /tmp/tmpndizli05.nii.gz
[2022-09-25 04:36:30,212] [393] [MainThread] [INFO] (monailabel.datastore.local:473) - Label Info: {'label_info': [{'name': 'spleen', 'idx': 1}, {'name': 'right kidney', 'idx': 2}, {'name': 'left kidney', 'idx': 3}, {'name': 'gallbladder', 'idx': 4}, {'name': 'esophagus', 'idx': 5}, {'name': 'liver', 'idx': 6}, {'name': 'stomach', 'idx': 7}, {'name': 'aorta', 'idx': 8}, {'name': 'inferior vena cava', 'idx': 9}, {'name': 'portal vein and splenic vein', 'idx': 10}, {'name': 'pancreas', 'idx': 11}, {'name': 'right adrenal gland', 'idx': 12}, {'name': 'left adrenal gland', 'idx': 13}], 'client_id': 'user-xyz', 'ts': 1664060790, 'checksum': 'SHA256:be4f651b196e6c8799deebee7718d2204c55ecd7af144ee7d11ce936e85c06ac', 'name': 'CV17056.nii.gz'}
[2022-09-25 04:36:30,214] [393] [MainThread] [INFO] (monailabel.interfaces.app:489) - New label saved for: CV17056 => CV17056
[2022-09-25 04:36:39,812] [393] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Train request: {'model': 'segmentation', 'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': True, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'client_id': 'user-xyz'}
[2022-09-25 04:36:39,812] [393] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:59) - COMMAND:: /home/amitjc/anaconda3/envs/monailabel-env/bin/python -m monailabel.interfaces.utils.app -m train -r {"model":"segmentation","name":"train_01","pretrained":true,"device":"cuda","max_epochs":50,"early_stop_patience":-1,"val_split":0.2,"train_batch_size":1,"val_batch_size":1,"multi_gpu":true,"gpus":"all","dataset":"SmartCacheDataset","dataloader":"ThreadDataLoader","client_id":"user-xyz"}
[2022-09-25 04:36:39,859] [446] [MainThread] [INFO] (__main__:38) - Initializing App from: /home/amitjc/apps/radiology; studies: /mnt/h/Cases/TMH/Liver; conf: {'models': 'segmentation'}
Failed to load image Python extension: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory
[2022-09-25 04:36:41,070] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-09-25 04:36:41,072] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2022-09-25 04:36:41,072] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2022-09-25 04:36:41,073] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2022-09-25 04:36:41,073] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2022-09-25 04:36:41,074] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2022-09-25 04:36:41,074] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2022-09-25 04:36:41,074] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2022-09-25 04:36:41,074] [446] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2022-09-25 04:36:41,075] [446] [MainThread] [INFO] (main:86) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2022-09-25 04:36:41,100] [446] [MainThread] [INFO] (main:90) - +++ Using Models: ['segmentation']
[2022-09-25 04:36:41,100] [446] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: /mnt/h/Cases/TMH/Liver
[2022-09-25 04:36:41,100] [446] [MainThread] [INFO] (monailabel.datastore.local:126) - Auto Reload: False; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (main:116) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x7feeaf66edf0>
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (main:172) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x7feeaf66edf0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7feea7102970>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7feea71029a0>}
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (main:185) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x7feea7102a30>
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/amitjc/.cache/monailabel/sessions
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:365) - Train Request (input): {'model': 'segmentation', 'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': True, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'client_id': 'user-xyz', 'local_rank': 0}
[2022-09-25 04:36:41,158] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:375) - CUDA_VISIBLE_DEVICES: None
[2022-09-25 04:36:41,166] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:380) - Distributed/Multi GPU is limited
[2022-09-25 04:36:41,166] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:395) - Distributed Training = FALSE
[2022-09-25 04:36:41,166] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:422) - 0 - Train Request (final): {'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': False, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'model': 'segmentation', 'client_id': 'user-xyz', 'local_rank': 0, 'run_id': '20220925_0436'}
[2022-09-25 04:36:41,166] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:521) - 0 - Using Device: cuda; IDX: None
[2022-09-25 04:36:41,167] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:343) - Total Records for Training: 1
[2022-09-25 04:36:41,167] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:344) - Total Records for Validation: 0
NVIDIA GeForce RTX 3090 with CUDA capability sm_86 is not compatible with the current PyTorch installation.
The current PyTorch install supports CUDA capabilities sm_37 sm_50 sm_60 sm_70.
If you want to use the NVIDIA GeForce RTX 3090 GPU with PyTorch, please check the instructions at https://pytorch.org/get-started/locally/
[2022-09-25 04:36:41,871] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:608) - 0 - Load Path /home/amitjc/apps/radiology/model/pretrained_segmentation.pt
Loading dataset:   0%|          | 0/1 [00:00<?, ?it/s]
Loading dataset: 100%|██████████| 1/1 [00:12<00:00, 12.42s/it]
Loading dataset: 100%|██████████| 1/1 [00:12<00:00, 12.42s/it]
cache_num is greater or equal than dataset length, fall back to regular monai.data.CacheDataset.
[2022-09-25 04:36:54,299] [446] [MainThread] [INFO] (monailabel.tasks.train.basic_train:228) - 0 - Records for Training: 1
[2022-09-25 04:36:54,302] [446] [MainThread] [INFO] (ignite.engine.engine.SupervisedTrainer:876) - Engine run resuming from iteration 0, epoch 0 until 50 epochs
[2022-09-25 04:36:54,346] [446] [MainThread] [INFO] (ignite.engine.engine.SupervisedTrainer:138) - Restored all variables from /home/amitjc/apps/radiology/model/pretrained_segmentation.pt
Exception in thread Thread-8:
Traceback (most recent call last):
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 90, in apply_transform
    return [_apply_transform(transform, item, unpack_items) for item in data]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 90, in <listcomp>
    return [_apply_transform(transform, item, unpack_items) for item in data]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 55, in _apply_transform
    return transform(parameters)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/spatial/dictionary.py", line 1227, in __call__
    d[key] = self.flipper(d[key])
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/spatial/array.py", line 765, in __call__
    out = self.forward_image(img, axes)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/spatial/array.py", line 756, in forward_image
    return torch.flip(img, axes)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/meta_tensor.py", line 249, in __torch_function__
    ret = super().__torch_function__(func, types, args, kwargs)
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/_tensor.py", line 1121, in __torch_function__
    ret = func(*args, **kwargs)
RuntimeError: CUDA error: no kernel image is available for execution on the device
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/threading.py", line 980, in _bootstrap_inner
    self.run()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/threading.py", line 917, in run
    self._target(*self._args, **self._kwargs)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/thread_buffer.py", line 48, in enqueue_values
    for src_val in self.src:
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 681, in __next__
    data = self._next_data()
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 721, in _next_data
    data = self._dataset_fetcher.fetch(index)  # may raise StopIteration
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 49, in <listcomp>
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/dataset.py", line 105, in __getitem__
    return self._transform(index)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/dataset.py", line 878, in _transform
    data = apply_transform(_transform, data)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 118, in apply_transform
    raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.spatial.dictionary.RandFlipd object at 0x7feea7583760>
Exception in thread Thread-9:
Traceback (most recent call last):
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 90, in apply_transform
    return [_apply_transform(transform, item, unpack_items) for item in data]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 90, in <listcomp>
    return [_apply_transform(transform, item, unpack_items) for item in data]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 55, in _apply_transform
    return transform(parameters)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/intensity/dictionary.py", line 421, in __call__
    d[key] = self.shifter(d[key], factor=factor, randomize=False)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/intensity/array.py", line 289, in __call__
    return self._shifter(img, self._offset if factor is None else self._offset * factor)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/intensity/array.py", line 236, in __call__
    out = img + offset
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/meta_tensor.py", line 249, in __torch_function__
    ret = super().__torch_function__(func, types, args, kwargs)
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/_tensor.py", line 1121, in __torch_function__
    ret = func(*args, **kwargs)
RuntimeError: CUDA error: no kernel image is available for execution on the device
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/threading.py", line 980, in _bootstrap_inner
    self.run()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/threading.py", line 917, in run
    self._target(*self._args, **self._kwargs)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/thread_buffer.py", line 48, in enqueue_values
    for src_val in self.src:
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 681, in __next__
    data = self._next_data()
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/dataloader.py", line 721, in _next_data
    data = self._dataset_fetcher.fetch(index)  # may raise StopIteration
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/amitjc/.local/lib/python3.9/site-packages/torch/utils/data/_utils/fetch.py", line 49, in <listcomp>
    data = [self.dataset[idx] for idx in possibly_batched_index]
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/dataset.py", line 105, in __getitem__
    return self._transform(index)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/data/dataset.py", line 878, in _transform
    data = apply_transform(_transform, data)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/transforms/transform.py", line 118, in apply_transform
    raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.intensity.dictionary.RandShiftIntensityd object at 0x7feea7583850>
Data iterator can not provide data anymore but required total number of iterations to run is not reached. Current iteration: 0 vs Total iterations to run : 50
[2022-09-25 04:36:54,629] [446] [MainThread] [ERROR] (ignite.engine.engine.SupervisedTrainer:992) - Engine run is terminating due to exception: the data to aggregate must be PyTorch Tensor.
[2022-09-25 04:36:54,629] [446] [MainThread] [ERROR] (ignite.engine.engine.SupervisedTrainer:178) - Exception: the data to aggregate must be PyTorch Tensor.
Traceback (most recent call last):
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 965, in _internal_run_as_gen
    self._fire_event(Events.EPOCH_COMPLETED)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/metrics/metric.py", line 329, in completed
    result = self.compute()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/handlers/ignite_metric.py", line 90, in compute
    result = self.metric_fn.aggregate()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/metrics/meandice.py", line 99, in aggregate
    raise ValueError("the data to aggregate must be PyTorch Tensor.")
ValueError: the data to aggregate must be PyTorch Tensor.
Traceback (most recent call last):
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 132, in <module>
    run_main()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 117, in run_main
    result = a.train(request)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/interfaces/app.py", line 416, in train
    result = task(request, self.datastore())
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/tasks/train/basic_train.py", line 396, in __call__
    res = self.train(0, world_size, req, datalist)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monailabel/tasks/train/basic_train.py", line 458, in train
    context.trainer.run()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/engines/trainer.py", line 53, in run
    super().run()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/engines/workflow.py", line 278, in run
    super().run(data=self.data_loader, max_epochs=self.state.max_epochs)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 892, in run
    return self._internal_run()
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 935, in _internal_run
    return next(self._internal_run_generator)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 993, in _internal_run_as_gen
    self._handle_exception(e)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 636, in _handle_exception
    self._fire_event(Events.EXCEPTION_RAISED, e)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/handlers/stats_handler.py", line 179, in exception_raised
    raise e
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 965, in _internal_run_as_gen
    self._fire_event(Events.EPOCH_COMPLETED)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/engine/engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "/home/amitjc/.local/lib/python3.9/site-packages/ignite/metrics/metric.py", line 329, in completed
    result = self.compute()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/handlers/ignite_metric.py", line 90, in compute
    result = self.metric_fn.aggregate()
  File "/home/amitjc/anaconda3/envs/monailabel-env/lib/python3.9/site-packages/monai/metrics/meandice.py", line 99, in aggregate
    raise ValueError("the data to aggregate must be PyTorch Tensor.")
ValueError: the data to aggregate must be PyTorch Tensor.
[2022-09-25 04:36:54,988] [393] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:77) - Return code: 1

RTX 3090 pytorch incompatibility error was returned; however,

conda list | grep "torch"

reveals

pytorch                   1.13.0.dev20220924 py3.9_cuda11.7_cudnn8.5.0_0    pytorch-nightly
pytorch-cuda              11.7                 h67b0de4_0    pytorch-nightly
pytorch-mutex             1.0                        cuda    pytorch-nightly
torchaudio                0.13.0.dev20220924      py39_cu117    pytorch-nightly
torchvision               0.13.1                   pypi_0    pypi

Monailabel server was deployed on wsl because, Ubuntu slicer monailabel module lacks "Train" and "Stop" tabs/buttons after deploying monailabel server on Ubuntu 22.04; issue raised over slicer forum

Monailabel server was also deployed successfully over powershell, however, training could not be done through this deployment either. Please find the logs below:

monailabel start_server --app apps/radiology --studies datasets/TMH/Liver/ --conf models segmentation
Using PYTHONPATH=C:\ProgramData\Anaconda3\envs;
""
2022-09-25 05:00:26,485 - USING:: version = False
2022-09-25 05:00:26,485 - USING:: app = N:\ApPz\MONAI\apps\radiology
2022-09-25 05:00:26,486 - USING:: studies = N:\ApPz\MONAI\datasets\TMH\Liver
2022-09-25 05:00:26,488 - USING:: verbose = INFO
2022-09-25 05:00:26,489 - USING:: conf = [['models', 'segmentation']]
2022-09-25 05:00:26,489 - USING:: host = 0.0.0.0
2022-09-25 05:00:26,490 - USING:: port = 8000
2022-09-25 05:00:26,494 - USING:: uvicorn_app = monailabel.app:app
2022-09-25 05:00:26,494 - USING:: ssl_keyfile = None
2022-09-25 05:00:26,495 - USING:: ssl_certfile = None
2022-09-25 05:00:26,495 - USING:: ssl_keyfile_password = None
2022-09-25 05:00:26,496 - USING:: ssl_ca_certs = None
2022-09-25 05:00:26,496 - USING:: workers = None
2022-09-25 05:00:26,496 - USING:: limit_concurrency = None
2022-09-25 05:00:26,497 - USING:: access_log = False
2022-09-25 05:00:26,497 - USING:: log_config = None
2022-09-25 05:00:26,497 - USING:: dryrun = False
2022-09-25 05:00:26,498 - USING:: action = start_server
2022-09-25 05:00:26,499 - ENV SETTINGS:: MONAI_LABEL_API_STR =
2022-09-25 05:00:26,499 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2022-09-25 05:00:26,499 - ENV SETTINGS:: MONAI_LABEL_APP_DIR =
2022-09-25 05:00:26,500 - ENV SETTINGS:: MONAI_LABEL_STUDIES =
2022-09-25 05:00:26,500 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2022-09-25 05:00:26,501 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB =
2022-09-25 05:00:26,501 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2022-09-25 05:00:26,504 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2022-09-25 05:00:26,507 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2022-09-25 05:00:26,508 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2022-09-25 05:00:26,511 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2022-09-25 05:00:26,512 - ENV SETTINGS:: MONAI_LABEL_DATASTORE =
2022-09-25 05:00:26,512 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL =
2022-09-25 05:00:26,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME =
2022-09-25 05:00:26,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD =
2022-09-25 05:00:26,513 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY =
2022-09-25 05:00:26,514 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH =
2022-09-25 05:00:26,514 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT =
2022-09-25 05:00:26,515 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH =
2022-09-25 05:00:26,515 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS =
2022-09-25 05:00:26,515 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME =
2022-09-25 05:00:26,516 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD =
2022-09-25 05:00:26,516 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH =
2022-09-25 05:00:26,517 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX =
2022-09-25 05:00:26,517 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX =
2022-09-25 05:00:26,517 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX =
2022-09-25 05:00:26,518 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2022-09-25 05:00:26,521 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2022-09-25 05:00:26,525 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2022-09-25 05:00:26,525 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2022-09-25 05:00:26,526 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2022-09-25 05:00:26,526 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2022-09-25 05:00:26,527 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2022-09-25 05:00:26,527 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2022-09-25 05:00:26,528 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2022-09-25 05:00:26,528 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH =
2022-09-25 05:00:26,529 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2022-09-25 05:00:26,529 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2022-09-25 05:00:26,529 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2022-09-25 05:00:26,530 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2022-09-25 05:00:26,530 -
Allow Origins: ['*']
[2022-09-25 05:00:27,327] [25360] [MainThread] [INFO] (uvicorn.error:75) - Started server process [25360]
[2022-09-25 05:00:27,328] [25360] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2022-09-25 05:00:27,328] [25360] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: N:\ApPz\MONAI\apps\radiology; studies: N:\ApPz\MONAI\datasets\TMH\Liver; conf: {'models': 'segmentation'}
[2022-09-25 05:00:27,392] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-09-25 05:00:27,408] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2022-09-25 05:00:27,408] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2022-09-25 05:00:27,409] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2022-09-25 05:00:27,411] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2022-09-25 05:00:27,412] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2022-09-25 05:00:27,413] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2022-09-25 05:00:27,418] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2022-09-25 05:00:27,419] [25360] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2022-09-25 05:00:27,421] [25360] [MainThread] [INFO] (main:86) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2022-09-25 05:00:27,463] [25360] [MainThread] [INFO] (main:90) - +++ Using Models: ['segmentation']
[2022-09-25 05:00:27,463] [25360] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: N:\ApPz\MONAI\datasets\TMH\Liver
[2022-09-25 05:00:27,465] [25360] [MainThread] [INFO] (monailabel.datastore.local:126) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2022-09-25 05:00:27,475] [25360] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-09-25 05:00:27,475] [25360] [MainThread] [INFO] (monailabel.datastore.local:146) - Start observing external modifications on datastore (AUTO RELOAD)
[2022-09-25 05:00:27,478] [25360] [MainThread] [INFO] (main:116) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x000002792556EB80>
[2022-09-25 05:00:27,479] [25360] [MainThread] [INFO] (main:172) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x000002792556EB80>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x0000027926507400>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x00000279265073D0>}
[2022-09-25 05:00:27,479] [25360] [MainThread] [INFO] (main:185) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x0000027926507EE0>
[2022-09-25 05:00:27,481] [25360] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\AMiT\.cache\monailabel\sessions
[2022-09-25 05:00:27,482] [25360] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-09-25 05:00:27,482] [25360] [MainThread] [INFO] (monailabel.interfaces.app:465) - App Init - completed
[2022-09-25 05:00:27,483] [timeloop] [INFO] Starting Timeloop..
[2022-09-25 05:00:27,483] [25360] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2022-09-25 05:00:27,484] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x00000279255FB1F0>
[2022-09-25 05:00:27,484] [25360] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x00000279255FB1F0>
[2022-09-25 05:00:27,485] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2022-09-25 05:00:27,485] [25360] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2022-09-25 05:00:27,489] [25360] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2022-09-25 05:00:27,490] [25360] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2022-09-25 05:02:10,277] [25360] [MainThread] [INFO] (monailabel.endpoints.datastore:100) - Saving Label for CV17056 for tag: final by admin
[2022-09-25 05:02:10,278] [25360] [MainThread] [INFO] (monailabel.endpoints.datastore:111) - Save Label params: {"label_info": [{"name": "Liver", "idx": 1}, {"name": "right kidney", "idx": 2}, {"name": "left kidney", "idx": 3}, {"name": "gallbladder", "idx": 4}, {"name": "esophagus", "idx": 5}, {"name": "stomach", "idx": 6}, {"name": "aorta", "idx": 7}, {"name": "inferior vena cava", "idx": 8}, {"name": "portal vein and splenic vein", "idx": 9}, {"name": "pancreas", "idx": 10}, {"name": "right adrenal gland", "idx": 11}, {"name": "left adrenal gland", "idx": 12}], "client_id": "user-xyz"}
[2022-09-25 05:02:10,279] [25360] [MainThread] [INFO] (monailabel.datastore.local:449) - Saving Label for Image: CV17056; Tag: final; Info: {'label_info': [{'name': 'Liver', 'idx': 1}, {'name': 'right kidney', 'idx': 2}, {'name': 'left kidney', 'idx': 3}, {'name': 'gallbladder', 'idx': 4}, {'name': 'esophagus', 'idx': 5}, {'name': 'stomach', 'idx': 6}, {'name': 'aorta', 'idx': 7}, {'name': 'inferior vena cava', 'idx': 8}, {'name': 'portal vein and splenic vein', 'idx': 9}, {'name': 'pancreas', 'idx': 10}, {'name': 'right adrenal gland', 'idx': 11}, {'name': 'left adrenal gland', 'idx': 12}], 'client_id': 'user-xyz'}
[2022-09-25 05:02:10,282] [25360] [MainThread] [INFO] (monailabel.datastore.local:457) - Adding Label: CV17056 => final => C:\Users\AMiT\AppData\Local\Temp\tmpo1idaxoj.nii.gz
[2022-09-25 05:02:10,289] [25360] [MainThread] [INFO] (monailabel.datastore.local:473) - Label Info: {'label_info': [{'name': 'Liver', 'idx': 1}, {'name': 'right kidney', 'idx': 2}, {'name': 'left kidney', 'idx': 3}, {'name': 'gallbladder', 'idx': 4}, {'name': 'esophagus', 'idx': 5}, {'name': 'stomach', 'idx': 6}, {'name': 'aorta', 'idx': 7}, {'name': 'inferior vena cava', 'idx': 8}, {'name': 'portal vein and splenic vein', 'idx': 9}, {'name': 'pancreas', 'idx': 10}, {'name': 'right adrenal gland', 'idx': 11}, {'name': 'left adrenal gland', 'idx': 12}], 'client_id': 'user-xyz', 'ts': 1664062330, 'checksum': 'SHA256:be4f651b196e6c8799deebee7718d2204c55ecd7af144ee7d11ce936e85c06ac', 'name': 'CV17056.nii.gz'}
[2022-09-25 05:02:10,291] [25360] [MainThread] [INFO] (monailabel.interfaces.app:489) - New label saved for: CV17056 => CV17056
[2022-09-25 05:02:20,220] [25360] [MainThread] [INFO] (monailabel.utils.async_tasks.task:36) - Train request: {'model': 'segmentation', 'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': True, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'client_id': 'user-xyz'}
[2022-09-25 05:02:20,222] [25360] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:59) - COMMAND:: C:\ProgramData\Anaconda3\envs\monailabel-env\python.exe -m monailabel.interfaces.utils.app -m train -r {"model":"segmentation","name":"train_01","pretrained":true,"device":"cuda","max_epochs":50,"early_stop_patience":-1,"val_split":0.2,"train_batch_size":1,"val_batch_size":1,"multi_gpu":true,"gpus":"all","dataset":"SmartCacheDataset","dataloader":"ThreadDataLoader","client_id":"user-xyz"}
[2022-09-25 05:02:20,328] [4396] [MainThread] [INFO] (__main__:38) - Initializing App from: N:\ApPz\MONAI\apps\radiology; studies: N:\ApPz\MONAI\datasets\TMH\Liver; conf: {'models': 'segmentation'}
[2022-09-25 05:02:22,635] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2022-09-25 05:02:22,645] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2022-09-25 05:02:22,645] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2022-09-25 05:02:22,645] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2022-09-25 05:02:22,646] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2022-09-25 05:02:22,646] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2022-09-25 05:02:22,647] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2022-09-25 05:02:22,647] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2022-09-25 05:02:22,648] [4396] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2022-09-25 05:02:22,648] [4396] [MainThread] [INFO] (main:86) - +++ Adding Model: segmentation => lib.configs.segmentation.Segmentation
[2022-09-25 05:02:22,674] [4396] [MainThread] [INFO] (main:90) - +++ Using Models: ['segmentation']
[2022-09-25 05:02:22,674] [4396] [MainThread] [INFO] (monailabel.interfaces.app:128) - Init Datastore for: N:\ApPz\MONAI\datasets\TMH\Liver
[2022-09-25 05:02:22,674] [4396] [MainThread] [INFO] (monailabel.datastore.local:126) - Auto Reload: False; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2022-09-25 05:02:22,680] [4396] [MainThread] [INFO] (monailabel.datastore.local:540) - Invalidate count: 0
[2022-09-25 05:02:22,680] [4396] [MainThread] [INFO] (main:116) - +++ Adding Inferer:: segmentation => <lib.infers.segmentation.Segmentation object at 0x0000026767A08400>
[2022-09-25 05:02:22,680] [4396] [MainThread] [INFO] (main:172) - {'segmentation': <lib.infers.segmentation.Segmentation object at 0x0000026767A08400>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x0000026769D73E50>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x0000026769D73E20>}
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (main:185) - +++ Adding Trainer:: segmentation => <lib.trainers.segmentation.Segmentation object at 0x0000026769D73EB0>
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: C:\Users\AMiT\.cache\monailabel\sessions
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:365) - Train Request (input): {'model': 'segmentation', 'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': True, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'client_id': 'user-xyz', 'local_rank': 0}
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:375) - CUDA_VISIBLE_DEVICES: None
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:380) - Distributed/Multi GPU is limited
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:395) - Distributed Training = FALSE
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:422) - 0 - Train Request (final): {'name': 'train_01', 'pretrained': True, 'device': 'cuda', 'max_epochs': 50, 'early_stop_patience': -1, 'val_split': 0.2, 'train_batch_size': 1, 'val_batch_size': 1, 'multi_gpu': False, 'gpus': 'all', 'dataset': 'SmartCacheDataset', 'dataloader': 'ThreadDataLoader', 'model': 'segmentation', 'client_id': 'user-xyz', 'local_rank': 0, 'run_id': '20220925_0502'}
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:521) - 0 - Using Device: cpu; IDX: None
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:343) - Total Records for Training: 1
[2022-09-25 05:02:22,681] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:344) - Total Records for Validation: 0
[2022-09-25 05:02:22,688] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:608) - 0 - Load Path N:\ApPz\MONAI\apps\radiology\model\pretrained_segmentation.pt
Loading dataset:   0%|          | 0/1 [00:00<?, ?it/s]
Loading dataset: 100%|##########| 1/1 [00:14<00:00, 14.51s/it]
Loading dataset: 100%|##########| 1/1 [00:14<00:00, 14.51s/it]
cache_num is greater or equal than dataset length, fall back to regular monai.data.CacheDataset.
[2022-09-25 05:02:37,202] [4396] [MainThread] [INFO] (monailabel.tasks.train.basic_train:228) - 0 - Records for Training: 1
torch.cuda.amp.GradScaler is enabled, but CUDA is not available.  Disabling.
[2022-09-25 05:02:37,205] [4396] [MainThread] [INFO] (ignite.engine.engine.SupervisedTrainer:876) - Engine run resuming from iteration 0, epoch 0 until 50 epochs
[2022-09-25 05:02:37,221] [4396] [MainThread] [ERROR] (ignite.engine.engine.SupervisedTrainer:992) - Engine run is terminating due to exception: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False. If you are running on a CPU-only machine, please use torch.load with map_location=torch.device('cpu') to map your storages to the CPU.
[2022-09-25 05:02:37,221] [4396] [MainThread] [ERROR] (ignite.engine.engine.SupervisedTrainer:178) - Exception: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False. If you are running on a CPU-only machine, please use torch.load with map_location=torch.device('cpu') to map your storages to the CPU.
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 946, in _internal_run_as_gen
    self._fire_event(Events.STARTED)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monai\handlers\checkpoint_loader.py", line 107, in __call__
    checkpoint = torch.load(self.load_path, map_location=self.map_location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 712, in load
    return _load(opened_zipfile, map_location, pickle_module, **pickle_load_args)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1049, in _load
    result = unpickler.load()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1019, in persistent_load
    load_tensor(dtype, nbytes, key, _maybe_decode_ascii(location))
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1001, in load_tensor
    wrap_storage=restore_location(storage, location),
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 175, in default_restore_location
    result = fn(storage, location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 152, in _cuda_deserialize
    device = validate_cuda_device(location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 136, in validate_cuda_device
    raise RuntimeError('Attempting to deserialize object on a CUDA '
RuntimeError: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False. If you are running on a CPU-only machine, please use torch.load with map_location=torch.device('cpu') to map your storages to the CPU.
Traceback (most recent call last):
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monailabel\interfaces\utils\app.py", line 132, in <module>
    run_main()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monailabel\interfaces\utils\app.py", line 117, in run_main
    result = a.train(request)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monailabel\interfaces\app.py", line 416, in train
    result = task(request, self.datastore())
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monailabel\tasks\train\basic_train.py", line 396, in __call__
    res = self.train(0, world_size, req, datalist)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monailabel\tasks\train\basic_train.py", line 458, in train
    context.trainer.run()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monai\engines\trainer.py", line 53, in run
    super().run()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monai\engines\workflow.py", line 278, in run
    super().run(data=self.data_loader, max_epochs=self.state.max_epochs)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 892, in run
    return self._internal_run()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 935, in _internal_run
    return next(self._internal_run_generator)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 993, in _internal_run_as_gen
    self._handle_exception(e)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 636, in _handle_exception
    self._fire_event(Events.EXCEPTION_RAISED, e)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monai\handlers\stats_handler.py", line 179, in exception_raised
    raise e
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 946, in _internal_run_as_gen
    self._fire_event(Events.STARTED)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\ignite\engine\engine.py", line 425, in _fire_event
    func(*first, *(event_args + others), **kwargs)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\monai\handlers\checkpoint_loader.py", line 107, in __call__
    checkpoint = torch.load(self.load_path, map_location=self.map_location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 712, in load
    return _load(opened_zipfile, map_location, pickle_module, **pickle_load_args)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1049, in _load
    result = unpickler.load()
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1019, in persistent_load
    load_tensor(dtype, nbytes, key, _maybe_decode_ascii(location))
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 1001, in load_tensor
    wrap_storage=restore_location(storage, location),
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 175, in default_restore_location
    result = fn(storage, location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 152, in _cuda_deserialize
    device = validate_cuda_device(location)
  File "C:\ProgramData\Anaconda3\envs\monailabel-env\lib\site-packages\torch\serialization.py", line 136, in validate_cuda_device
    raise RuntimeError('Attempting to deserialize object on a CUDA '
RuntimeError: Attempting to deserialize object on a CUDA device but torch.cuda.is_available() is False. If you are running on a CPU-only machine, please use torch.load with map_location=torch.device('cpu') to map your storages to the CPU.
[2022-09-25 05:02:37,573] [25360] [ThreadPoolExecutor-0_0] [INFO] (monailabel.utils.async_tasks.utils:77) - Return code: 1

Look forward to guidance for working with monai.

Thanks again.

Best Regards, Amit.

Dear Sachidanand,

First of all I would like to thank and congratulate you for your tremendous work. AI for healthcare imaging has never been more accessible.

I am a medical physicist in radiotherapy department in Amsterdam. I am currently investigating the possibilities of deep learning based segmentation in adaptive radiotherapy using MRI images. I've been using/developing monailabel APP (deep_edit multilabel app) for a while and so far I'm very happy with it.

However, I have encountered a few issues and have not been able to resolve them and I hope you can help me with that;

• This app generates labels with a (default) deviating position ( x: -2, y: -2, z: -2). Maybe this is because of a transform or something else do you have an idea how I can solve this?

-I use this app to segment different organs in the abdomen. The results are very good for 8 of the 9 organs (dice > 0.95), but for the duodenum it is much lower. Is there an opportunity within monailabel to put more focus on improving a single structure.

• Is there a possibility to automatically export the created labels in Dicom-RT file structure.

Kind Regards

OB

Describe the bug Slicer shows the automatic label with a different origin. Apparently, it is related to the way ITK interprets the nifty header. From this discussion, it seems nibabel and nifty differ in the way they interpret the nifty header (https://github.com/nipy/nibabel/issues/863)

CC @wyli

To Reproduce Using the Fusion Challenge dataset MICCAI 2012 (OASIS project) to train highresnet for Brain parcellation.

Fusion Challenge dataset MICCAI 2012: 35 brain MRI scans obtained from the OASIS project. The manual brain segmentations of these images were produced by Neuromorphometrics, Inc. (http://Neuromorphometrics.com/) using the brainCOLOR labeling protocol.

Expected behavior To show the label in the same origin as the original image

Screenshots The workaround for this is to first change the affine of images and labels. Then use MONAI Label to train the model. See the affine changes in the following images

Original Affine:

Modified affine:

Is your feature request related to a problem? Please describe. MONAI v0.6.0rc1 is available: https://pypi.org/project/monai/0.6.0rc1/

this ticket tracks any issues with the new version of MONAI and verifies that the new features are usable:

• load MMAR pretrained https://github.com/Project-MONAI/MONAI/blob/0.6.0rc1/monai/apps/mmars/mmars.py#L204-L207
• dynamic datalist there are breaking changes since 0.5.x, we'll release demos https://github.com/Project-MONAI/MONAI/issues/2402

cc @Nic-Ma @yiheng-wang-nv

Minor improvement to DICOMWeb datastore:

• Now uses pydicom-seg in favor of dcmqi_tools's binary segimage2itkimage for conversion of DICOM-SEGs to ITK images
• Now supports multiclass conversion

Signed-off-by: masadcv [email protected]

I have update and released binary for torchmaxflow (https://github.com/masadcv/torchmaxflow) which can now be used for scribbles. It has pre-built windows binaries so will resolve issues reported in https://github.com/Project-MONAI/MONAILabel/issues/719

This PR restores scribbles functionality using graphcut method from torchmaxflow. This PR still has issue as reported in https://github.com/Project-MONAI/MONAILabel/discussions/713 It will be resolved with merging of an on-going PR #717 once this is merged.

In various projects I have noticed that the speed at which the next sample is determined by the "Random" strategy depends strongly on the total number of studies in the datastore, i.e. it takes up to 10 s when having 2,000 unlabeled studies in the store. I consider this to be a great drawback for the user experience.

The time bottleneck originates from the following for-loop which is used to get further information on every unlabeled image. This information is then used to retrieve the image's last timestamp in order to generate an image-specific weight: https://github.com/Project-MONAI/MONAILabel/blob/cb8421c4991a351468d0f2487601b02ec6911944/monailabel/tasks/activelearning/random.py#L39-L43

All unlabeled images' weights are then used to determine one random image out of all unlabeled images: https://github.com/Project-MONAI/MONAILabel/blob/cb8421c4991a351468d0f2487601b02ec6911944/monailabel/tasks/activelearning/random.py#L45

Now I wonder if we need this time intense weighting in a random draw at all? Probably this is very valid for small datastores to avoid repeated image selections. But in larger datastores this won't play a role. What do you think about a PR that deactivates weighting if a user-specified number of unlabeled images is available(i.e. > 50 images)? Or is there a more time-efficient way to determine the weights?

Thank you for your marvelous work!

While using QuPath with your plugin in training my annotations, I received errors. Please help in solving these errors.

[2022-12-28 21:03:17,778] [191288] [MainThread] [INFO] (monailabel.utils.async_tasks.task:41) - Train request: {'model': 'ss', 'train_batch_size': 10, 'val_batch_size': 10} [2022-12-28 21:03:17,778] [191288] [ThreadPoolExecutor-2_0] [INFO] (monailabel.utils.async_tasks.utils:49) - Before:: /miniconda3/envs: [2022-12-28 21:03:17,779] [191288] [ThreadPoolExecutor-2_0] [INFO] (monailabel.utils.async_tasks.utils:53) - After:: /miniconda3/envs: [2022-12-28 21:03:17,779] [191288] [ThreadPoolExecutor-2_0] [INFO] (monailabel.utils.async_tasks.utils:65) - COMMAND:: /miniconda3/envs/p39/bin/python -m monailabel.interfaces.utils.app -m train -r {"model":"ss","train_batch_size":10,"val_batch_size":10,"gpus":"all"} [2022-12-28 21:03:17,878] [202303] [MainThread] [INFO] (main:38) - Initializing App from: /MONAILabel/monailabel/apps/pathology; studies: /MONAILabel/monailabel/datasets/pathology; conf: {} [2022-12-28 21:03:19,114] [202303] [MainThread] [INFO] (numexpr.utils:148) - Note: NumExpr detected 24 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8. [2022-12-28 21:03:19,114] [202303] [MainThread] [INFO] (numexpr.utils:160) - NumExpr defaulting to 8 threads. [2022-12-28 21:03:20,654] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'> [2022-12-28 21:03:20,657] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_nuclei.SegmentationNuclei'> [2022-12-28 21:03:20,658] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.nuclick.NuClick'> [2022-12-28 21:03:20,658] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.hovernet_nuclei.HovernetNuclei'> [2022-12-28 21:03:20,658] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.ss.SegmentationNuclei'> [2022-12-28 21:03:20,658] [202303] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.classification_nuclei.ClassificationNuclei'> [2022-12-28 21:03:20,658] [202303] [MainThread] [INFO] (main:83) - +++ Adding Model: classification_nuclei => lib.configs.classification_nuclei.ClassificationNuclei [2022-12-28 21:03:21,073] [202303] [MainThread] [INFO] (main:83) - +++ Adding Model: hovernet_nuclei => lib.configs.hovernet_nuclei.HovernetNuclei [2022-12-28 21:03:21,148] [202303] [MainThread] [INFO] (main:83) - +++ Adding Model: nuclick => lib.configs.nuclick.NuClick [2022-12-28 21:03:21,211] [202303] [MainThread] [INFO] (main:83) - +++ Adding Model: ss => lib.configs.ss.SegmentationNuclei [2022-12-28 21:03:21,279] [202303] [MainThread] [INFO] (main:83) - +++ Adding Model: segmentation_nuclei => lib.configs.segmentation_nuclei.SegmentationNuclei [2022-12-28 21:03:21,325] [202303] [MainThread] [INFO] (main:87) - +++ Using Models: ['classification_nuclei', 'hovernet_nuclei', 'nuclick', 'ss', 'segmentation_nuclei'] [2022-12-28 21:03:21,325] [202303] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: /MONAILabel/monailabel/datasets/pathology [2022-12-28 21:03:21,325] [202303] [MainThread] [INFO] (monailabel.datastore.local:129) - Auto Reload: False; Extensions: ['.nii.gz', '.nii', '.nrrd', '.jpg', '.png', '.tif', '.svs', '.xml'] [2022-12-28 21:03:21,327] [202303] [MainThread] [INFO] (monailabel.datastore.local:576) - Invalidate count: 0 [2022-12-28 21:03:21,483] [202303] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: classification_nuclei => <lib.infers.classification_nuclei.ClassificationNuclei object at 0x7f29d0a49100> [2022-12-28 21:03:21,883] [202303] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: hovernet_nuclei => <lib.infers.hovernet_nuclei.HovernetNuclei object at 0x7f29ae3176a0> [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: nuclick => <lib.infers.nuclick.NuClick object at 0x7f299bb10a60> [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (lib.configs.ss:102) - Using Preload: False; ROI Size: [8192819281920, 8192819281920] [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: ss => <lib.infers.segmentation_nuclei.SegmentationNuclei object at 0x7f2990d99ee0> [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (lib.configs.segmentation_nuclei:88) - Using Preload: False; ROI Size: [1024, 1024] [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (main:129) - +++ Adding Inferer:: segmentation_nuclei => <lib.infers.segmentation_nuclei.SegmentationNuclei object at 0x7f29903d6e80> [2022-12-28 21:03:21,941] [202303] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: classification_nuclei => <lib.trainers.classification_nuclei.ClassificationNuclei object at 0x7f29903d6fa0> [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: hovernet_nuclei => <lib.trainers.hovernet_nuclei.HovernetNuclei object at 0x7f29903d6f70> [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: nuclick => <lib.trainers.nuclick.NuClick object at 0x7f2990360bb0> [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: ss => <lib.trainers.segmentation_nuclei.SegmentationNuclei object at 0x7f2990360eb0> [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (main:153) - +++ Adding Trainer:: segmentation_nuclei => <lib.trainers.segmentation_nuclei.SegmentationNuclei object at 0x7f2990360ee0> [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (main:174) - Active Learning Strategies:: ['wsi_random'] [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /root/.cache/monailabel/sessions [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600 [2022-12-28 21:03:21,942] [202303] [MainThread] [INFO] (monailabel.tasks.train.basic_train:432) - Train Request (input): {'model': 'ss', 'train_batch_size': 10, 'val_batch_size': 10, 'gpus': 'all', 'local_rank': 0} [2022-12-28 21:03:21,943] [202303] [MainThread] [INFO] (monailabel.tasks.train.basic_train:442) - CUDA_VISIBLE_DEVICES: None [2022-12-28 21:03:21,943] [202303] [MainThread] [INFO] (monailabel.tasks.train.basic_train:605) - Running cleanup... [2022-12-28 21:03:21,943] [202303] [MainThread] [INFO] (lib.utils:90) - Split data based on tile size: (512, 512); groups: {'CC': 1, 'll': 2, 'hh': 3} BasicUNet features: (32, 64, 128, 256, 512, 32). BasicUNet features: (32, 64, 128, 256, 512, 32). BasicUNet features: (32, 64, 128, 256, 512, 32). 0%| | 0/7 [00:00<?, ?it/s][2022-12-28 21:03:21,944] [202303] [MainThread] [INFO] (lib.utils:550) - ++ Using Groups: {'CC': 1, 'll': 2, 'hh': 3} [2022-12-28 21:03:21,944] [202303] [MainThread] [INFO] (lib.utils:552) - Fetching Image/Label : {'image': '/MONAILabel/monailabel/datasets/pathology/PPPP.png', 'label': '/MONAILabel/monailabel/datasets/pathology/labels/final/PPPP.xml'} [2022-12-28 21:03:22,129] [202303] [MainThread] [INFO] (lib.utils:560) - Total Points: 18458 [2022-12-28 21:03:22,133] [202303] [MainThread] [INFO] (lib.utils:562) - ID: PPPP => Groups: dict_keys(['CC', 'll', 'hh']); Location: (1990, 350); Size: 3077 x 6109 [2022-12-28 21:03:22,946] [202303] [MainThread] [INFO] (lib.utils:616) - Image => Input: (6864, 5312, 3); Total Patches to save: 154 [2022-12-28 21:03:33,933] [202303] [MainThread] [INFO] (lib.utils:593) - CC => p: 0; c: 1; unique: (array([0], dtype=uint8), array([36461568])) [2022-12-28 21:03:34,288] [202303] [MainThread] [INFO] (lib.utils:593) - ll => p: 14; c: 2; unique: (array([0, 2], dtype=uint8), array([35428467, 1033101])) [2022-12-28 21:03:34,636] [202303] [MainThread] [INFO] (lib.utils:593) - hh => p: 0; c: 3; unique: (array([0, 2], dtype=uint8), array([35428467, 1033101])) [2022-12-28 21:03:34,636] [202303] [MainThread] [INFO] (lib.utils:616) - Label => Input: (6864, 5312); Total Patches to save: 154 14%|█▍ | 1/7 [00:12<01:17, 12.91s/it][2022-12-28 21:03:34,850] [202303] [MainThread] [INFO] (lib.utils:550) - ++ Using Groups: {'CC': 1, 'll': 2, 'hh': 3} [2022-12-28 21:03:34,850] [202303] [MainThread] [INFO] (lib.utils:552) - Fetching Image/Label : {'image': '/MONAILabel/monailabel/datasets/pathology/PPPP.png', 'label': '/MONAILabel/monailabel/datasets/pathology/labels/final/PPPP.xml'} [2022-12-28 21:03:35,376] [202303] [MainThread] [INFO] (lib.utils:560) - Total Points: 85424 [2022-12-28 21:03:35,393] [202303] [MainThread] [INFO] (lib.utils:562) - ID: PPPP => Groups: dict_keys(['CC', 'll', 'hh']); Location: (-1289, -586); Size: 34681 x 16388 [2022-12-28 21:03:35,393] [202303] [MainThread] [WARNING] (lib.utils:565) - Reducing Region to Max-Width; w: 34681; max_w: 10240 [2022-12-28 21:03:35,393] [202303] [MainThread] [WARNING] (lib.utils:568) - Reducing Region to Max-Height; h: 16388; max_h: 10240 14%|█▍ | 1/7 [00:13<01:20, 13.45s/it] Traceback (most recent call last): File "/miniconda3/envs/p39/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/miniconda3/envs/p39/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/miniconda3/envs/p39/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 132, in run_main() File "/miniconda3/envs/p39/lib/python3.9/site-packages/monailabel/interfaces/utils/app.py", line 117, in run_main result = a.train(request) File "/miniconda3/envs/p39/lib/python3.9/site-packages/monailabel/interfaces/app.py", line 429, in train result = task(request, self.datastore()) File "/miniconda3/envs/p39/lib/python3.9/site-packages/monailabel/tasks/train/basic_train.py", line 444, in call datalist = self.pre_process(req, datastore) File "/MONAILabel/monailabel/apps/pathology/lib/trainers/segmentation_nuclei.py", line 74, in pre_process return split_dataset( File "/MONAILabel/monailabel/apps/pathology/lib/utils.py", line 99, in split_dataset ds_new.extend(split_local_dataset(datastore, d, output_dir, groups, tile_size, max_region)) File "/MONAILabel/monailabel/apps/pathology/lib/utils.py", line 261, in split_local_dataset img = Image.open(d["image"]).convert("RGB") File "/miniconda3/envs/p39/lib/python3.9/site-packages/PIL/Image.py", line 3172, in open im = _open_core(fp, filename, prefix, formats) File "/miniconda3/envs/p39/lib/python3.9/site-packages/PIL/Image.py", line 3159, in _open_core _decompression_bomb_check(im.size) File "/miniconda3/envs/p39/lib/python3.9/site-packages/PIL/Image.py", line 3068, in _decompression_bomb_check raise DecompressionBombError( PIL.Image.DecompressionBombError: Image size (445833922 pixels) exceeds limit of 178956970 pixels, could be decompression bomb DOS attack. [2022-12-28 21:03:36,205] [191288] [ThreadPoolExecutor-2_0] [INFO] (monailabel.utils.async_tasks.utils:83) - Return code: 1

I would appreciate any help. Best.

Is your feature request related to a problem? Please describe. Due to the complexities required by the creation of interfaces for the backend and frontend to interact the "information" flow within MONAI Label is heavily offuscated and hard to comprehend for development.

Describe the solution you'd like Create the following four animations/figures:

• An UML-like figure of MONAI Label that is specific for the backend to complement the existing REST API one.
• Three transition animations that exemplify how you move from X to MONAI Label, where X is:
  • Pure Pytorch
  • Ignite
  • MONAI

The last point is inspired by the PyTorch Lighting animation which conveys a lot of information in a very succinct way.

Additional context This came to be after I had explained MONAI Label to @MichelaA and a while ago Ignite to @diazandr3s. This would facilitate a faster and better understanding of MONAI Label and hopefully as a side-effect less issue.

Furthermore, this falls in line with the style of tutorials that are available in MONAI Core and it would be highly useful due to the fact that MONAI Label borrows design from PyTorch Lighting ultimately merging two very different APIs together which leads to a steep learning curve.

Discussed in https://github.com/Project-MONAI/MONAILabel/discussions/1190

^{Originally posted by orenlivne December 8, 2022} I'm trying to annotate pathology images using monai within DSA. Any advice on fixing it would be greatly appreciated. Thank you.

Problem

1. An annotation (inference) MONAILabel server call from the DSA GUI fails inside _name_to_id, probably due to a wrong image path. When the infer method calls _name_to_id, it does not return anything inside the foreach loop, which returns an ID, name tuple. The fallback is returning the name only, causing the stack trace. This means _name_to_id has a small bug in its last line, but my real issue is that the input name to it is somehow wrong in the workflow I created.
2. The DSA monai annotation is very slow (30-40s before it finally calls the infer function and crashes), even for a small ROI of 400x200 pixels. Could be related to the wrong image path issue.

Monailabel source dsa.py

    def _name_to_id(self, name):
        folders = self.folders if self.folders else self._get_all_folders()
        ###### I added the following two lines for debugging, cf. logs below:
        logger.info(f"name: {name}")
        logger.info(f"folders: {folders}")
        
        for folder in folders:
            data = self.gc.get("item", parameters={"folderId": folder, "limit": 0})
            for d in data:
                if d.get("largeImage") and d["name"] == name or Path(d["name"]).stem == name:
                    return d["_id"], d["name"].  ###### nothing must have been returned during this loop.**
        return name  ###### So this fallback is called and causes an exception since a tuple is expected by the caller.**

MONAILabel Server Stack Trace:

File "/Users/oren/monai/MONAILabel/monailabel/endpoints/wsi_infer.py", line 126, in api_run_wsi_inference
    return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output)
  File "/Users/oren/monai/MONAILabel/monailabel/endpoints/wsi_infer.py", line 110, in run_wsi_inference
    result = instance.infer_wsi(request)
  File "/Users/oren/monai/MONAILabel/monailabel/interfaces/app.py", line 633, in infer_wsi
    image = datastore.get_image_uri(request["image"])
  File "/Users/oren/monai/MONAILabel/monailabel/datastore/dsa.py", line 152, in get_image_uri
    image_id, name = self._name_to_id(image_id)
ValueError: too many values to unpack (expected 2)

Steps to Reproduce

Hardware: Apple Air, Apple M1 CPU, Monterey MacOS. Note that in the steps below I fixed two bugs specific to M1 + docker that I comment on, but are not relevant to the current discussion.

• Install OpenSlide: brew install openslide.
• Find the location of the openslide dylib: brew info openslide | grep Cellar | awk {'print $1}') and set to an environment variable. On Monterey, this is export OPENSLIDE_LIB=opt/homebrew/Cellar/openslide/3.4.1_7/lib
• Install DSA. Add the line chmod g+w /var/run/docker.sock 2>/dev/null to start_girder.sh (BUG 1). Run DSA via docker-compose.
• DSA is running on localhost:8080.
• Within a conda env, install monailabel from weekly release with pip install monailabel-weekly (note: the main release pip package is broken for Apple M1 due to bad package numpymaxflow==0.0.2 which leads numpy wheel building to fail; the weekly release upgraded to 0.0.5, which works).
• Download the monai pathology app.
• Note that DYLD_LIBRARY_PATHcannot be passed to a script if SIP is enabled on MacOS and thus OpenSlide won't be recognized by the monailabel server(BUG 2). Thus, start the monailabel server script with an additional line dynamically added to it that sets the library path, with the command tmpfile=$(mktemp /tmp/monailabel.XXXXXX) && ( cat $(which monailabel) | awk -v n=2 -v s="export DYLD_LIBRARY_PATH=\"${OPENSLIDE_LIB}\"" 'NR == n {print s} {print}' > ${tmpfile} ) && chmod +x ${tmpfile} && ( ${tmpfile} start_server --app $HOME/out/pathology --studies http://0.0.0.0:8080/api/v1 ) ; rm ${tmpfile}.
• Install the monai DSA plugin:
• Download the monai DSA plugin docker image: docker pull projectmonai/monailabel-dsa. Install it using the Slicer CLI Web under DSA admin plugins.
• Open the HistomicsUI, open image, select ROI, set ** MONAILabel Address: http://host.docker.internal:8000/ (note: if localhost:8080 is used here, the job will fail on Permission Denied; this is the appropriate docker address on Mac). ** Model Name: segmentation_nuclei.

DSA Job Log

Title:MONAILabel Annotations on sample-image.tiff
Type:projectmonai/monailabel-dsa:latest#MONAILabelAnnotation
Job ID:6391e73bf5e935c6e8bcb171
Status: ERROR
Timeline:
0 s163.411 s
Created:December 8, 2022 at 8:31:39
Scheduled start:December 8, 2022 at 8:31:39
Last update:December 8, 2022 at 8:34:22
Log output:
[2022-12-08 13:34:19,563] INFO: Running container: image: projectmonai/[email protected]:99c7a31b0be9790205efa2327b38a8bf8583d4cab71a157ddbbdf0812e69f100 args: ['MONAILabelAnnotation', '--analysis_level', '0', '--analysis_roi', '14967, 19208, 451, 217', '--analysis_tile_size', '1024', '--api-url', 'http://girder:8080/api/v1/', '--extra_params', '{}', '--girder-token', 'd9C4qgeV3sEku4QT6xLM6ecMsQCABJ2gOLE2k2qmWLOWaOy5J99W1CSB6wicLwNG', '--min_fgnd_frac', '-1', '--min_poly_area', '80', '--model_name', 'segmentation_nuclei', '--server', 'http://host.docker.internal:8000/', '/mnt/girder_worker/2e6ee16dbe1f4d86abbc4b9cc8e32dba/sample-image.tiff', '/mnt/girder_worker/2e6ee16dbe1f4d86abbc4b9cc8e32dba/MONAILabel Annotations-outputAnnotationFile.anot'] runtime: None kwargs: {'tty': False, 'volumes': {'/var/folders/zw/c2j1_twn3_g09ldg5frh0pmm0000gn/T/tmpjb3ekwrq': {'bind': '/mnt/girder_worker/2e6ee16dbe1f4d86abbc4b9cc8e32dba', 'mode': 'rw'}}, 'detach': True, 'network': 'container:4ec6011efa66054d0e9310701f107d5019de73d95f08a651484582a0f640dd67'}
INFO:root:CLI Parameters ...

INFO:root:USING:: inputImageFile = /mnt/girder_worker/2e6ee16dbe1f4d86abbc4b9cc8e32dba/sample-image.tiff
INFO:root:USING:: outputAnnotationFile = /mnt/girder_worker/2e6ee16dbe1f4d86abbc4b9cc8e32dba/MONAILabel Annotations-outputAnnotationFile.anot
INFO:root:USING:: analysis_level = 0
INFO:root:USING:: analysis_roi = [14967.0, 19208.0, 451.0, 217.0]
INFO:root:USING:: analysis_tile_size = 1024.0
INFO:root:USING:: girderApiUrl = http://girder:8080/api/v1/
INFO:root:USING:: extra_params = {}
INFO:root:USING:: girderToken = d9C4qgeV3sEku4QT6xLM6ecMsQCABJ2gOLE2k2qmWLOWaOy5J99W1CSB6wicLwNG
INFO:root:USING:: min_fgnd_frac = -1.0
INFO:root:USING:: min_poly_area = 80.0
INFO:root:USING:: model_name = segmentation_nuclei
INFO:root:USING:: server = http://host.docker.internal:8000/
INFO:root:>> Reading input image ... 

INFO:root:Run MONAILabel Task... and collect the annotations: [14967.0, 19208.0] => [451.0, 217.0]
INFO:root:For Server Logs click/open:  http://host.docker.internal:8000/logs/?refresh=3
Traceback (most recent call last):
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 174, in <module>
    main(CLIArgumentParser().parse_args())
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 168, in main
    fetch_annotations(args, tiles)
  File "/opt/monailabel/dsa/cli/MONAILabelAnnotation/MONAILabelAnnotation.py", line 55, in fetch_annotations
    _, res = client.wsi_infer(model=args.model_name, image_in=image, body=body, output=output)
  File "/opt/monailabel/dsa/cli/client.py", line 188, in wsi_infer
    raise MONAILabelClientException(
cli.client.MONAILabelClientException: (2, "Status: 500; Response: b'Internal Server Error'")
DockerException: Non-zero exit code from docker container (1).
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 451, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 87, in __call__
    super().__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 337, in __call__
    super(DockerTask, self).__call__(*args, **kwargs)
  File "/opt/girder_worker/girder_worker/task.py", line 154, in __call__
    results = super(Task, self).__call__(*_t_args, **_t_kwargs)
  File "/opt/venv/lib/python3.9/site-packages/celery/app/trace.py", line 734, in __protected_call__
    return self.run(*args, **kwargs)
  File "/opt/slicer_cli_web/slicer_cli_web/girder_worker_plugin/direct_docker_run.py", line 123, in run
    return _docker_run(task, **kwargs)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 405, in _docker_run
    _run_select_loop(task, container, read_streams, write_streams)
  File "/opt/girder_worker/girder_worker/docker/tasks/__init__.py", line 251, in _run_select_loop
    raise DockerException('Non-zero exit code from docker container (%d).' % exit_code)
Keyword arguments:
{
  "container_args": [
    "MONAILabelAnnotation",
    "--analysis_level",
    "0",
    "--analysis_roi",
    "14967, 19208, 451, 217",
    "--analysis_tile_size",
    "1024",
    "--api-url",
    "<slicer_cli_web.girder_worker_plugin.direct_docker_run.GirderApiUrl object at 0x41958da550>",
    "--extra_params",
    "{}",
    "--girder-token",
    "<slicer_cli_web.girder_worker_plugin.direct_docker_run.GirderToken object at 0x42891d5280>",
    "--min_fgnd_frac",
    "-1",
    "--min_poly_area",
    "80",
    "--model_name",
    "segmentation_nuclei",
    "--server",
    "http://host.docker.internal:8000/",
    "<slicer_cli_web.girder_worker_plugin.direct_docker_run.DirectGirderFileIdToVolume: File ID=6391ba8af5e935c6e8bcb152 -> \"sample-image.tiff\">",
    "<girder_worker.docker.transforms.VolumePath: \"MONAILabel Annotations-outputAnnotationFile.anot\">"
  ],
  "image": "projectmonai/m[email protected]:99c7a31b0be9790205efa2327b38a8bf8583d4cab71a157ddbbdf0812e69f100",
  "pull_image": "if-not-present"
}

MONAILabel Server Logs

[2022-12-08 08:31:09,012] [60736] [MainThread] [INFO] (monailabel.interfaces.app:468) - App Init - completed [2022-12-08 08:31:09,012] [60736] [MainThread] [INFO] (timeloop:60) - Starting Timeloop.. [2022-12-08 08:31:09,013] [60736] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete..run_scheduler at 0x16b3d7e20> [2022-12-08 08:31:09,013] [60736] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set [2022-12-08 08:34:22,032] [60736] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:108) - WSI Infer Request: {'model': 'segmentation_nuclei', 'image': 'sample-image', 'output': 'dsa', 'level': 0, 'location': [14967, 19208], 'size': [451, 217], 'tile_size': [1024, 1024], 'min_poly_area': 80, 'wsi_tiles': []} [2022-12-08 08:34:22,165] [60736] [MainThread] [INFO] (monailabel.datastore.dsa:138) - name: sample-image [2022-12-08 08:34:22,165] [60736] [MainThread] [INFO] (monailabel.datastore.dsa:139) - folders: ['63865dff31e1eb24754d2e99', '63865dd1f37a980298fa9ce9']

Note the two lines I added, showing the name and folders inside _name_to_id.

MONAILabel Server Screen Output

[2022-12-08 08:31:09,013] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set                           
[2022-12-08 08:31:09,013] [60736] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set 
[2022-12-08 08:31:09,013] [60736] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.                            
[2022-12-08 08:31:09,013] [60736] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to 
quit)                                                                                                                               
[2022-12-08 08:34:22,032] [60736] [MainThread] [INFO] (monailabel.endpoints.wsi_infer:108) - WSI Infer Request: {'model': 'segmentat
ion_nuclei', 'image': 'sample-image', 'output': 'dsa', 'level': 0, 'location': [14967, 19208], 'size': [451, 217], 'tile_size': [102
4, 1024], 'min_poly_area': 80, 'wsi_tiles': []}
[2022-12-08 08:34:22,165] [60736] [MainThread] [INFO] (monailabel.datastore.dsa:138) - name: sample-image                  
[2022-12-08 08:34:22,165] [60736] [MainThread] [INFO] (monailabel.datastore.dsa:139) - folders: ['63865dff31e1eb24754d2e99', '63865d
d1f37a980298fa9ce9']                                                                                                                
[2022-12-08 08:34:22,227] [60736] [MainThread] [ERROR] (uvicorn.error:369) - Exception in ASGI application
Traceback (most recent call last):                                                                                                  
  File "/Users/oren/monai/MONAILabel/monailabel/datastore/dsa.py", line 150, in get_image_uri
    name = self.get_image_info(image_id)["name"]                                                                                    
  File "/Users/oren/monai/MONAILabel/monailabel/datastore/dsa.py", line 176, in get_image_info
    return self.gc.getItem(image_id)  # type: ignore                                                                                
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/girder_client/__init__.py", line 619, in getItem
    return self.getResource('item', itemId)                                                                                         
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/girder_client/__init__.py", line 519, in getResource
    return self.get(route)                                                                                                          
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/girder_client/__init__.py", line 471, in get
    return self.sendRestRequest('GET', path, parameters, jsonResp=jsonResp)                                   
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/girder_client/__init__.py", line 463, in sendRestRequest
    raise HttpError(                                                                                                                
girder_client.HttpError: HTTP error 400: GET http://0.0.0.0:8080/api/v1/item/sample-image
Response text: {"field": "id", "message": "Invalid ObjectId: sample-image", "type": "validation"}                              
 During handling of the above exception, another exception occurred:                                        
                                                                                                                                    
Traceback (most recent call last):                                                                                                  
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/uvicorn/protocols/http/h11_impl.py", line 366, in run_asgi
    result = await app(self.scope, self.receive, self.send)                                                                         
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/fastapi/applications.py", line 269, in __call__
    await super().__call__(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/applications.py", line 124, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/middleware/errors.py", line 184, in __call__
    raise exc
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/middleware/errors.py", line 162, in __call__
    await self.app(scope, receive, _send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/middleware/cors.py", line 84, in __call__
    await self.app(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/exceptions.py", line 93, in __call__
    raise exc
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/exceptions.py", line 82, in __call__
    await self.app(scope, receive, sender)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/fastapi/middleware/asyncexitstack.py", line 21, in __call__
    raise e
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/fastapi/middleware/asyncexitstack.py", line 18, in __call__
    await self.app(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/routing.py", line 670, in __call__
    await route.handle(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/routing.py", line 266, in handle
    await self.app(scope, receive, send)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/starlette/routing.py", line 65, in app
    response = await func(request)
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/fastapi/routing.py", line 227, in app
    raw_response = await run_endpoint_function(
  File "/Users/oren/miniconda3/envs/monai2/lib/python3.10/site-packages/fastapi/routing.py", line 160, in run_endpoint_function
    return await dependant.call(**values)
  File "/Users/oren/monai/MONAILabel/monailabel/endpoints/wsi_infer.py", line 126, in api_run_wsi_inference
    return run_wsi_inference(background_tasks, model, image, session_id, None, wsi, output)
  File "/Users/oren/monai/MONAILabel/monailabel/endpoints/wsi_infer.py", line 110, in run_wsi_inference
    result = instance.infer_wsi(request)
  File "/Users/oren/monai/MONAILabel/monailabel/interfaces/app.py", line 633, in infer_wsi
    image = datastore.get_image_uri(request["image"])
  File "/Users/oren/monai/MONAILabel/monailabel/datastore/dsa.py", line 152, in get_image_uri
    image_id, name = self._name_to_id(image_id)
ValueError: too many values to unpack (expected 2)
```</div>

0.6.0 

Describe the bug In the codebase (here, here and here) the threshold of 0.5 is used disregarding the number of labels.

Expected behavior The threshold should be 1/(len(labels)-1). Such that for a 3-class problem (besides background) the threshold is 0.33.

At the moment we are asking the models to be extra sure of the labels before considering them right. This might be useful but is not explicitly implemented and is worse and worse the more classes there are.

Describe the bug I have encountered two different situations where monai label is using far more memory than I would expect. Are these user errors, or related to my dataset? Has monai label been designed with scalability in mind?

1. When I push train, my entire dataset is loaded into CPU RAM. Our dataset is larger than some of the competition datasets (BTCV or MSD) but not extremely large - roughly 100 CT scans that are 512x512xH, where H is usually in the range of about 500. Uncompressed, that adds up to nearly 100GB, which leads to the program crashing. Is there an option to avoid loading all data into RAM, and just load it on demand? Perhaps using pre-fetch to avoid creating a bottleneck? Since I am using the segmentation model, which trains on patches, perhaps it would be sufficient to load just the patches into RAM, rather than the full images?

In case it is relevant, my dataset has 12 foreground labels.

My work around solution is to use swap, but obviously that's not ideal.

2. After training, clicking RUN gives me another OOM error. I tried decreasing the roi_size for my model, but even at 64x64x64 I'm still exceeding the 8GB of GPU VRAM available:

For 128x128x128

torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 8.25 GiB (GPU 0; 7.92 GiB total capacity; 440.46 MiB already allocated; 6.63 GiB free; 610.00 MiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF

For 96x96x96

torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 7.62 GiB (GPU 0; 7.92 GiB total capacity; 1.20 GiB already allocated; 5.46 GiB free; 1.77 GiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF

For 64x64x64

torch.cuda.OutOfMemoryError: CUDA out of memory. Tried to allocate 7.62 GiB (GPU 0; 7.92 GiB total capacity; 1.20 GiB already allocated; 5.46 GiB free; 1.77 GiB reserved in total by PyTorch) If reserved memory is >> allocated memory try setting max_split_size_mb to avoid fragmentation.  See documentation for Memory Management and PYTORCH_CUDA_ALLOC_CONF

It might be expected behaviour for deepedit models to cause an OOM, since they run on the full image. However, I expected that a segmentation model would scale to arbitrary sized images, because it analyses the image in patches. Have I misunderstood something? Or is the stitching of the patches also carried out in the GPU?

To Reproduce Steps to reproduce the behavior:

1. Get hold of a medium sized dataset with ground truth labels. Put them in a folder structure as expected by monai. Hold back the ground truth labels for at least one for step 6.
2. Make a copy of the radiology/lib/config/segmentation.py file (e.g. segmentation_custom.py) and modify the foreground classes and roi_size.
3. Run the monailabel app:

monailabel start_server --app radiology --studies relative/path/to/images --conf models segmentation_custom --conf use_pretrained_model false

5. In Slicer, connect to the server and click Train.
6. If you have enough CPU RAM and training completes, click Next Sample to get an unlabelled image and then Run to automatically generate labels.

Expected behavior I expected to be able to train a network and run inference on a dataset with an arbitrary number of arbitrarily sized images.

I've used 128x128x128 patches with nnunet, and been able to run inference on GPUs with only 4GB of VRAM. I'm surprised that an 8GB GPU gets an OOM when trying to run the segmentation network with 64x64x64 patches.

8GB of GPU memory was enough to train the network, so I assumed it would also be enough to run inference.

Screenshots N/A

Environment

Ensuring you use the relevant python executable, please paste the output of:

python -c 'import monai; monai.config.print_debug_info()'

================================
Printing MONAI config...
================================
MONAI version: 1.0.1
Numpy version: 1.23.4
Pytorch version: 1.13.0+cu117
MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False
MONAI rev id: 8271a193229fe4437026185e218d5b06f7c8ce69
MONAI __file__: /home/chris/Software/monai/venv/lib/python3.8/site-packages/monai/__init__.py

Optional dependencies:
Pytorch Ignite version: 0.4.10
Nibabel version: 4.0.2
scikit-image version: 0.19.3
Pillow version: 9.3.0
Tensorboard version: 2.11.0
gdown version: 4.5.3
TorchVision version: 0.14.0+cu117
tqdm version: 4.64.1
lmdb version: 1.3.0
psutil version: 5.9.4
pandas version: NOT INSTALLED or UNKNOWN VERSION.
einops version: 0.6.0
transformers version: NOT INSTALLED or UNKNOWN VERSION.
mlflow version: NOT INSTALLED or UNKNOWN VERSION.
pynrrd version: 0.4.3

For details about installing the optional dependencies, please visit:
    https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies


================================
Printing system config...
================================
System: Linux
Linux version: Ubuntu 20.04.5 LTS
Platform: Linux-5.14.0-1054-oem-x86_64-with-glibc2.29
Processor: x86_64
Machine: x86_64
Python version: 3.8.10
Process name: python
Command: ['python', '-c', 'import monai; monai.config.print_debug_info()']
Open files: []
Num physical CPUs: 6
Num logical CPUs: 12
Num usable CPUs: 12
CPU usage (%): [16.5, 22.2, 15.4, 25.0, 20.9, 82.1, 13.4, 10.5, 12.3, 12.3, 13.9, 15.2]
CPU freq. (MHz): 1579
Load avg. in last 1, 5, 15 mins (%): [11.6, 10.4, 26.0]
Disk usage (%): 81.0
Avg. sensor temp. (Celsius): UNKNOWN for given OS
Total physical memory (GB): 31.0
Available memory (GB): 28.3
Used memory (GB): 2.2

================================
Printing GPU config...
================================
Num GPUs: 1
Has CUDA: True
CUDA version: 11.7
cuDNN enabled: True
cuDNN version: 8500
Current device: 0
Library compiled for CUDA architectures: ['sm_37', 'sm_50', 'sm_60', 'sm_70', 'sm_75', 'sm_80', 'sm_86']
GPU 0 Name: NVIDIA GeForce GTX 1080
GPU 0 Is integrated: False
GPU 0 Is multi GPU board: False
GPU 0 Multi processor count: 20
GPU 0 Total memory (GB): 7.9
GPU 0 CUDA capability (maj.min): 6.1

Additional context N/A