# MonaiLabel vertebrae segmentation sample-app doesn't work for sample data

**URL:** <https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243>\
**Category:** Support\
**Tags:** monailabel\
**Created:** [January 14, 2023, 9:11pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243 "2023-01-14T21:11:17Z")\
**Posts on this page:** 13\
**Page:** 1

<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 14, 2023, 9:11pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/1 "2023-01-14T21:11:17Z")

</div>

After clicking Run Auto Segmentation, the segments of the segmentationNode are still empty.

 ![Captura desde 2023-01-14 18-05-19](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/8/084cdcbc9f21b6f20a6655b28424db88989b0b6e.jpeg)

Another CT I tried only segmented half a vertebrae.

If I try segmentation\_vertebrae model instead the monai-label server crashes

Here is the console output for localization\_spine

```auto
~$ monailabel start_server --app /home/user1/Escritorio/Monai/apps/radiology --studies /home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr --conf models "localization_spine,localization_vertebra,segmentation_vertebra"
Using PYTHONPATH=/home/user1:

2023-01-14 17:57:49,144 - USING:: version = False
2023-01-14 17:57:49,144 - USING:: app = /home/user1/Escritorio/Monai/apps/radiology
2023-01-14 17:57:49,144 - USING:: studies = /home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr
2023-01-14 17:57:49,144 - USING:: verbose = INFO
2023-01-14 17:57:49,144 - USING:: conf = [['models', 'localization_spine,localization_vertebra,segmentation_vertebra']]
2023-01-14 17:57:49,144 - USING:: host = 0.0.0.0
2023-01-14 17:57:49,144 - USING:: port = 8000
2023-01-14 17:57:49,144 - USING:: uvicorn_app = monailabel.app:app
2023-01-14 17:57:49,144 - USING:: ssl_keyfile = None
2023-01-14 17:57:49,144 - USING:: ssl_certfile = None
2023-01-14 17:57:49,144 - USING:: ssl_keyfile_password = None
2023-01-14 17:57:49,144 - USING:: ssl_ca_certs = None
2023-01-14 17:57:49,144 - USING:: workers = None
2023-01-14 17:57:49,144 - USING:: limit_concurrency = None
2023-01-14 17:57:49,144 - USING:: access_log = False
2023-01-14 17:57:49,144 - USING:: log_config = None
2023-01-14 17:57:49,144 - USING:: dryrun = False
2023-01-14 17:57:49,144 - USING:: action = start_server
2023-01-14 17:57:49,144 - ENV SETTINGS:: MONAI_LABEL_API_STR = 
2023-01-14 17:57:49,144 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 
2023-01-14 17:57:49,145 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2023-01-14 17:57:49,145 - 
Allow Origins: ['*']
[2023-01-14 17:57:49,432] [850291] [MainThread] [INFO] (uvicorn.error:75) - Started server process [850291]
[2023-01-14 17:57:49,432] [850291] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-01-14 17:57:49,432] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/user1/Escritorio/Monai/apps/radiology; studies: /home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr; conf: {'models': 'localization_spine,localization_vertebra,segmentation_vertebra'}
[2023-01-14 17:57:49,455] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-01-14 17:57:49,458] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2023-01-14 17:57:49,459] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-01-14 17:57:49,460] [850291] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-01-14 17:57:49,460] [850291] [MainThread] [INFO] (main:93) - +++ Adding Model: localization_spine => lib.configs.localization_spine.LocalizationSpine
[2023-01-14 17:57:49,564] [850291] [MainThread] [INFO] (main:93) - +++ Adding Model: localization_vertebra => lib.configs.localization_vertebra.LocalizationVertebra
[2023-01-14 17:57:49,648] [850291] [MainThread] [INFO] (main:93) - +++ Adding Model: segmentation_vertebra => lib.configs.segmentation_vertebra.SegmentationVertebra
[2023-01-14 17:57:49,733] [850291] [MainThread] [INFO] (main:96) - +++ Using Models: ['localization_spine', 'localization_vertebra', 'segmentation_vertebra']
[2023-01-14 17:57:49,733] [850291] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: /home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr
[2023-01-14 17:57:49,733] [850291] [MainThread] [INFO] (monailabel.datastore.local:129) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2023-01-14 17:57:49,734] [850291] [MainThread] [INFO] (monailabel.datastore.local:593) - Adding New Image: CTChest => CTChest.nii.gz
[2023-01-14 17:57:49,734] [850291] [MainThread] [INFO] (monailabel.datastore.local:576) - Invalidate count: 1
[2023-01-14 17:57:49,735] [850291] [MainThread] [INFO] (monailabel.datastore.local:150) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: localization_spine => <lib.infers.localization_spine.LocalizationSpine object at 0x7fb1700a5f30>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: localization_vertebra => <lib.infers.localization_vertebra.LocalizationVertebra object at 0x7fb16cb0d480>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: segmentation_vertebra => <lib.infers.segmentation_vertebra.SegmentationVertebra object at 0x7fb16cb0d4b0>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:191) - {'localization_spine': <lib.infers.localization_spine.LocalizationSpine object at 0x7fb1700a5f30>, 'localization_vertebra': <lib.infers.localization_vertebra.LocalizationVertebra object at 0x7fb16cb0d480>, 'segmentation_vertebra': <lib.infers.segmentation_vertebra.SegmentationVertebra object at 0x7fb16cb0d4b0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7fb16cb0e560>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7fb16cb0e590>, 'vertebra_pipeline': <lib.infers.vertebra_pipeline.InferVertebraPipeline object at 0x7fb16cb0e5f0>}
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: localization_spine => <lib.trainers.localization_spine.LocalizationSpine object at 0x7fb16cb0d8d0>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: localization_vertebra => <lib.trainers.localization_vertebra.LocalizationVertebra object at 0x7fb16cb0d780>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: segmentation_vertebra => <lib.trainers.segmentation_vertebra.SegmentationVertebra object at 0x7fb16cb0d7e0>
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/user1/.cache/monailabel/sessions
[2023-01-14 17:57:49,736] [850291] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (monailabel.interfaces.app:475) - App Init - completed
[2023-01-14 17:57:49,737] [timeloop] [INFO] Starting Timeloop..
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-01-14 17:57:49,737] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7fb16d05cc10>
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7fb16d05cc10>
[2023-01-14 17:57:49,737] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2023-01-14 17:57:49,737] [850291] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2023-01-14 17:58:05,865] [850291] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {'strategy': 'random', 'client_id': 'user-xyz'}
[2023-01-14 17:58:05,865] [850291] [MainThread] [INFO] (monailabel.tasks.activelearning.random:47) - Random: Selected Image: CTChest; Weight: 6180
[2023-01-14 17:58:05,865] [850291] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {'id': 'CTChest', 'weight': 6180, 'path': '/home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr/CTChest.nii.gz', 'ts': 1673729869, 'name': 'CTChest.nii.gz'}
[2023-01-14 17:58:13,440] [850291] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'localization_spine', 'image': 'CTChest', 'device': 'cpu', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2023-01-14 17:58:13,440] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:279) - Infer Request (final): {'device': 'cpu', 'model': 'localization_spine', 'image': '/home/user1/Escritorio/Monai/datasets/vertebrae/imagesTr/CTChest.nii.gz', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz', 'description': 'A pre-trained model for volumetric (3D) spine localization from CT image'}
[2023-01-14 17:58:13,441] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2023-01-14 17:58:13,441] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path']
[2023-01-14 17:58:15,869] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (LoadImaged): Time: 2.4272; image: torch.Size([512, 512, 139])(torch.float32)
[2023-01-14 17:58:15,870] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureTyped): Time: 0.0009; image: torch.Size([512, 512, 139])(torch.float32)
[2023-01-14 17:58:15,870] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureChannelFirstd): Time: 0.0001; image: torch.Size([1, 512, 512, 139])(torch.float32)
[2023-01-14 17:58:15,884] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (CacheObjectd): Time: 0.0134; image: torch.Size([1, 512, 512, 139])(torch.float32)
[2023-01-14 17:58:16,779] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Spacingd): Time: 0.8947; image: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 17:58:16,836] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityRanged): Time: 0.0569; image: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 17:58:17,448] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (GaussianSmoothd): Time: 0.6115; image: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 17:58:17,494] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityd): Time: 0.0461; image: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 17:58:17,494] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:471) - Inferer:: cpu => SlidingWindowInferer => {'roi_size': (96, 96, 96), 'sw_batch_size': 2, 'overlap': 0.4, 'mode': gaussian, 'sigma_scale': 0.125, 'padding_mode': 'replicate', 'cval': 0.0, 'sw_device': None, 'device': None, 'progress': False, 'cpu_thresh': None, 'roi_weight_map': None}
[2023-01-14 17:58:17,494] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:420) - Infer model path: /home/user1/Escritorio/Monai/apps/radiology/model/pretrained_localization_spine.pt
[2023-01-14 18:00:39,455] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - POST - Run Transform(s)
[2023-01-14 18:00:39,455] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - POST - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path', 'image_meta_dict', 'latencies', 'image_cached', 'pred']
[2023-01-14 18:00:39,455] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (EnsureTyped): Time: 0.0001; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([25, 300, 300, 266])(torch.float32)
[2023-01-14 18:00:39,759] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Activationsd): Time: 0.3031; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([25, 300, 300, 266])(torch.float32)
[2023-01-14 18:00:42,576] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (AsDiscreted): Time: 2.8175; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 18:00:42,839] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (KeepLargestConnectedComponentd): Time: 0.2623; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 18:00:42,844] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (BinaryMaskd): Time: 0.0051; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([1, 300, 300, 266])(torch.float32)
[2023-01-14 18:00:42,938] [850291] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Restored): Time: 0.094; image: torch.Size([1, 300, 300, 266])(torch.float32); pred: torch.Size([512, 512, 139])(torch.float32)
[2023-01-14 18:00:43,013] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:571) - Writing Result...
[2023-01-14 18:00:43,014] [850291] [MainThread] [INFO] (monailabel.transform.writer:189) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2023-01-14 18:00:43,213] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:334) - ++ Latencies => Total: 149.7728; Pre: 4.0537; Inferer: 141.9601; Invert: 0.0000; Post: 3.5590; Write: 0.1997
[2023-01-14 18:00:43,213] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:358) - Result File: /tmp/tmpt87i1c7f.nrrd
[2023-01-14 18:00:43,213] [850291] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:359) - Result Json Keys: ['label_names', 'latencies']

```

Thanks for the help

---

<div class="post-metadata">

**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 20, 2023, 3:55pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/2 "2023-01-20T15:55:51Z")

</div>

Hi

The server does work for sample radiology app “segmentation\_spleen” on the same virtualenviroment

 ![Captura desde 2023-01-20 12-16-22](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/8/c87b95d9bd26bba21d0cc21e26757e780fcb68ad.jpeg)

```auto
~/Escritorio/Monai$ monailabel start_server --app apps/radiology --studies datasets/Task09_Spleen/imagesTr --conf models segmentation_spleen
Using PYTHONPATH=/home/user1:

2023-01-20 12:13:57,337 - USING:: version = False
2023-01-20 12:13:57,337 - USING:: app = /home/user1/Escritorio/Monai/apps/radiology
2023-01-20 12:13:57,337 - USING:: studies = /home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr
2023-01-20 12:13:57,337 - USING:: verbose = INFO
2023-01-20 12:13:57,337 - USING:: conf = [['models', 'segmentation_spleen']]
2023-01-20 12:13:57,337 - USING:: host = 0.0.0.0
2023-01-20 12:13:57,337 - USING:: port = 8000
2023-01-20 12:13:57,337 - USING:: uvicorn_app = monailabel.app:app
2023-01-20 12:13:57,337 - USING:: ssl_keyfile = None
2023-01-20 12:13:57,337 - USING:: ssl_certfile = None
2023-01-20 12:13:57,337 - USING:: ssl_keyfile_password = None
2023-01-20 12:13:57,337 - USING:: ssl_ca_certs = None
2023-01-20 12:13:57,337 - USING:: workers = None
2023-01-20 12:13:57,337 - USING:: limit_concurrency = None
2023-01-20 12:13:57,337 - USING:: access_log = False
2023-01-20 12:13:57,337 - USING:: log_config = None
2023-01-20 12:13:57,337 - USING:: dryrun = False
2023-01-20 12:13:57,337 - USING:: action = start_server
2023-01-20 12:13:57,337 - ENV SETTINGS:: MONAI_LABEL_API_STR = 
2023-01-20 12:13:57,337 - ENV SETTINGS:: MONAI_LABEL_PROJECT_NAME = MONAILabel
2023-01-20 12:13:57,337 - ENV SETTINGS:: MONAI_LABEL_APP_DIR = 
2023-01-20 12:13:57,337 - ENV SETTINGS:: MONAI_LABEL_STUDIES = 
2023-01-20 12:13:57,337 - ENV SETTINGS:: MONAI_LABEL_AUTH_ENABLE = False
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_AUTH_DB = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_APP_CONF = '{}'
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TASKS_TRAIN = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TASKS_STRATEGY = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TASKS_SCORING = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TASKS_BATCH_INFER = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_URL = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_USERNAME = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PASSWORD = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_API_KEY = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_CACHE_PATH = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_PROJECT = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_ASSET_PATH = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_DSA_ANNOTATION_GROUPS = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_USERNAME = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PASSWORD = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_PATH = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_QIDO_PREFIX = None
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_WADO_PREFIX = None
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_STOW_PREFIX = None
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_FETCH_BY_FRAME = False
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CONVERT_TO_NIFTI = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_SEARCH_FILTER = '{"Modality": "CT"}'
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_CACHE_EXPIRY = 180
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_PROXY_TIMEOUT = 30.0
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DICOMWEB_READ_TIMEOUT = 5.0
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_AUTO_RELOAD = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_READ_ONLY = False
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_DATASTORE_FILE_EXT = '["*.nii.gz", "*.nii", "*.nrrd", "*.jpg", "*.png", "*.tif", "*.svs", "*.xml"]'
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_SERVER_PORT = 8000
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_CORS_ORIGINS = '[]'
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_SESSIONS = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_SESSION_PATH = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_SESSION_EXPIRY = 3600
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_INFER_CONCURRENCY = -1
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_INFER_TIMEOUT = 600
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TRACKING_ENABLED = True
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_TRACKING_URI = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_ZOO_SOURCE = github
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_ZOO_REPO = Project-MONAI/model-zoo/hosting_storage_v1
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_ZOO_AUTH_TOKEN = 
2023-01-20 12:13:57,338 - ENV SETTINGS:: MONAI_LABEL_AUTO_UPDATE_SCORING = True
2023-01-20 12:13:57,338 - 
Allow Origins: ['*']
[2023-01-20 12:13:57,611] [1927570] [MainThread] [INFO] (uvicorn.error:75) - Started server process [1927570]
[2023-01-20 12:13:57,611] [1927570] [MainThread] [INFO] (uvicorn.error:45) - Waiting for application startup.
[2023-01-20 12:13:57,611] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.app:38) - Initializing App from: /home/user1/Escritorio/Monai/apps/radiology; studies: /home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr; conf: {'models': 'segmentation_spleen'}
[2023-01-20 12:13:57,636] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for MONAILabelApp Found: <class 'main.MyApp'>
[2023-01-20 12:13:57,638] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_3d.Deepgrow3D'>
[2023-01-20 12:13:57,639] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepedit.DeepEdit'>
[2023-01-20 12:13:57,639] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_vertebra.LocalizationVertebra'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_spleen.SegmentationSpleen'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.deepgrow_2d.Deepgrow2D'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation_vertebra.SegmentationVertebra'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.segmentation.Segmentation'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.class_utils:37) - Subclass for TaskConfig Found: <class 'lib.configs.localization_spine.LocalizationSpine'>
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (main:93) - +++ Adding Model: segmentation_spleen => lib.configs.segmentation_spleen.SegmentationSpleen
[2023-01-20 12:13:57,640] [1927570] [MainThread] [INFO] (monailabel.utils.others.generic:185) - Downloading resource: /home/user1/Escritorio/Monai/apps/radiology/model/pretrained_segmentation_spleen.pt from https://github.com/Project-MONAI/MONAILabel/releases/download/pretrained/radiology_segmentation_unet_spleen.pt
pretrained_segmentation_spleen.pt: 18.4MB [00:06, 3.09MB/s]                                                                                                                                                              
2023-01-20 12:14:03,890 - INFO - Downloaded: /home/user1/Escritorio/Monai/apps/radiology/model/pretrained_segmentation_spleen.pt
2023-01-20 12:14:03,890 - INFO - Expected md5 is None, skip md5 check for file /home/user1/Escritorio/Monai/apps/radiology/model/pretrained_segmentation_spleen.pt.
[2023-01-20 12:14:04,938] [1927570] [MainThread] [INFO] (lib.configs.segmentation_spleen:75) - EPISTEMIC Enabled: False; Samples: 5
[2023-01-20 12:14:04,938] [1927570] [MainThread] [INFO] (main:96) - +++ Using Models: ['segmentation_spleen']
[2023-01-20 12:14:04,938] [1927570] [MainThread] [INFO] (monailabel.interfaces.app:135) - Init Datastore for: /home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr
[2023-01-20 12:14:04,939] [1927570] [MainThread] [INFO] (monailabel.datastore.local:129) - Auto Reload: True; Extensions: ['*.nii.gz', '*.nii', '*.nrrd', '*.jpg', '*.png', '*.tif', '*.svs', '*.xml']
[2023-01-20 12:14:04,943] [1927570] [MainThread] [INFO] (monailabel.datastore.local:576) - Invalidate count: 0
[2023-01-20 12:14:04,943] [1927570] [MainThread] [INFO] (monailabel.datastore.local:150) - Start observing external modifications on datastore (AUTO RELOAD)
[2023-01-20 12:14:04,943] [1927570] [MainThread] [INFO] (main:126) - +++ Adding Inferer:: segmentation_spleen => <lib.infers.segmentation_spleen.SegmentationSpleen object at 0x7f3ed429dfc0>
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (main:191) - {'segmentation_spleen': <lib.infers.segmentation_spleen.SegmentationSpleen object at 0x7f3ed429dfc0>, 'Histogram+GraphCut': <monailabel.scribbles.infer.HistogramBasedGraphCut object at 0x7f3ed3d1e6b0>, 'GMM+GraphCut': <monailabel.scribbles.infer.GMMBasedGraphCut object at 0x7f3ed3d1e6e0>}
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (main:206) - +++ Adding Trainer:: segmentation_spleen => <lib.trainers.segmentation_spleen.SegmentationSpleen object at 0x7f3ed3d982e0>
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (monailabel.utils.sessions:51) - Session Path: /home/user1/.cache/monailabel/sessions
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (monailabel.utils.sessions:52) - Session Expiry (max): 3600
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (monailabel.interfaces.app:475) - App Init - completed
[2023-01-20 12:14:04,944] [timeloop] [INFO] Starting Timeloop..
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (timeloop:60) - Starting Timeloop..
[2023-01-20 12:14:04,944] [timeloop] [INFO] Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f3ed3d0ee60>
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (timeloop:42) - Registered job <function MONAILabelApp.on_init_complete.<locals>.run_scheduler at 0x7f3ed3d0ee60>
[2023-01-20 12:14:04,944] [timeloop] [INFO] Timeloop now started. Jobs will run based on the interval set
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (timeloop:63) - Timeloop now started. Jobs will run based on the interval set
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (uvicorn.error:59) - Application startup complete.
[2023-01-20 12:14:04,944] [1927570] [MainThread] [INFO] (uvicorn.error:206) - Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
[2023-01-20 12:14:40,865] [1927570] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {'strategy': 'first', 'client_id': 'user-xyz'}
[2023-01-20 12:14:40,865] [1927570] [MainThread] [INFO] (monailabel.tasks.activelearning.first:38) - First: Selected Image: spleen_10
[2023-01-20 12:14:40,868] [1927570] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {'id': 'spleen_10', 'path': '/home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr/spleen_10.nii.gz', 'ts': 1673700860, 'name': 'spleen_10.nii.gz', 'strategy': {'first': {'ts': 1674227680, 'client_id': 'user-xyz'}}}
[2023-01-20 12:14:53,752] [1927570] [MainThread] [INFO] (monailabel.endpoints.activelearning:43) - Active Learning Request: {'strategy': 'first', 'client_id': 'user-xyz'}
[2023-01-20 12:14:53,752] [1927570] [MainThread] [INFO] (monailabel.tasks.activelearning.first:38) - First: Selected Image: spleen_10
[2023-01-20 12:14:53,754] [1927570] [MainThread] [INFO] (monailabel.endpoints.activelearning:59) - Next sample: {'id': 'spleen_10', 'path': '/home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr/spleen_10.nii.gz', 'ts': 1673700860, 'name': 'spleen_10.nii.gz', 'strategy': {'first': {'ts': 1674227693, 'client_id': 'user-xyz'}}}
[2023-01-20 12:15:01,791] [1927570] [MainThread] [INFO] (monailabel.endpoints.infer:160) - Infer Request: {'model': 'segmentation_spleen', 'image': 'spleen_10', 'device': 'cpu', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz'}
[2023-01-20 12:15:01,791] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:279) - Infer Request (final): {'device': 'cpu', 'model': 'segmentation_spleen', 'image': '/home/user1/Escritorio/Monai/datasets/Task09_Spleen/imagesTr/spleen_10.nii.gz', 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'client_id': 'user-xyz', 'description': 'A pre-trained model for volumetric (3D) segmentation of the spleen from CT image'}
[2023-01-20 12:15:01,792] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2023-01-20 12:15:01,792] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path']
[2023-01-20 12:15:02,083] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (LoadImaged): Time: 0.2906; image: torch.Size([512, 512, 55])(torch.float32)
[2023-01-20 12:15:02,084] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureTyped): Time: 0.0002; image: torch.Size([512, 512, 55])(torch.float32)
[2023-01-20 12:15:02,084] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureChannelFirstd): Time: 0.0001; image: torch.Size([1, 512, 512, 55])(torch.float32)
[2023-01-20 12:15:04,614] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Spacingd): Time: 2.53; image: torch.Size([1, 500, 500, 271])(torch.float32)
[2023-01-20 12:15:04,797] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityRanged): Time: 0.1831; image: torch.Size([1, 500, 500, 271])(torch.float32)
[2023-01-20 12:15:04,798] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:471) - Inferer:: cpu => SlidingWindowInferer => {'roi_size': (160, 160, 160), 'sw_batch_size': 1, 'overlap': 0.25, 'mode': constant, 'sigma_scale': 0.125, 'padding_mode': constant, 'cval': 0.0, 'sw_device': None, 'device': None, 'progress': False, 'cpu_thresh': None, 'roi_weight_map': None}
[2023-01-20 12:15:04,798] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:420) - Infer model path: /home/user1/Escritorio/Monai/apps/radiology/model/pretrained_segmentation_spleen.pt
[2023-01-20 12:15:17,355] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - POST - Run Transform(s)
[2023-01-20 12:15:17,355] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - POST - Input Keys: ['device', 'model', 'image', 'result_extension', 'result_dtype', 'client_id', 'description', 'image_path', 'image_meta_dict', 'latencies', 'pred']
[2023-01-20 12:15:17,356] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (EnsureTyped): Time: 0.0001; image: torch.Size([1, 500, 500, 271])(torch.float32); pred: torch.Size([2, 500, 500, 271])(torch.float32)
[2023-01-20 12:15:17,420] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Activationsd): Time: 0.0644; image: torch.Size([1, 500, 500, 271])(torch.float32); pred: torch.Size([2, 500, 500, 271])(torch.float32)
[2023-01-20 12:15:22,801] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (AsDiscreted): Time: 5.3802; image: torch.Size([1, 500, 500, 271])(torch.float32); pred: torch.Size([1, 500, 500, 271])(torch.float32)
[2023-01-20 12:15:22,858] [1927570] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Restored): Time: 0.0571; image: torch.Size([1, 500, 500, 271])(torch.float32); pred: torch.Size([512, 512, 55])(torch.float32)
[2023-01-20 12:15:22,885] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:571) - Writing Result...
[2023-01-20 12:15:22,886] [1927570] [MainThread] [INFO] (monailabel.transform.writer:189) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2023-01-20 12:15:24,913] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:334) - ++ Latencies => Total: 23.1218; Pre: 3.0060; Inferer: 12.5575; Invert: 0.0000; Post: 5.5303; Write: 2.0278
[2023-01-20 12:15:24,913] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:358) - Result File: /tmp/tmpq5s1_hsr.nrrd
[2023-01-20 12:15:24,913] [1927570] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:359) - Result Json Keys: ['label_names', 'latencies']

```

Could someone help? or give pointers?

Thanks a lot

---

<div class="post-metadata">

**Author:** ![rbumm](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/rbumm/32/9404_2.png) [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Post date:** [January 21, 2023, 11:55pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/3 "2023-01-21T23:55:55Z")

</div>

@diazandr3s can maybe comment and will present vertrebrae segmentation with 3D Slicer sample datasets in the upcoming [MONAILabel workshop](https://projectweek.na-mic.org/PW38_2023_GranCanaria/MONAILabel_Workshop.html) on **Wednesday January 25th 9-11am EST**

---

<div class="post-metadata">

**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 22, 2023, 1:32am UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/4 "2023-01-22T01:32:28Z")

</div>

Thanks for the ping, @rbumm.

@mau_igna_06:

The vertebra segmentation model has been trained on a portion of the VerSe dataset. This means the model may need training to work on other datasets.

Can you try the **localization\_vertebra** or **vertebra\_pipeline**? It should be under the list of Auto Segmentation models.

You may also be interested on the whole-body CT segmentation model that includes vertebra segmentation. This model was trained on the Total Segmentator dataset.

Here you can find the app folder: [radiology\_full\_ct-upgraded-HYBRID - Google Drive](https://drive.google.com/drive/folders/17eJan-8_oNCnZyJk8B9zLQpwaOjtDuKi?usp=share_link)

Please let us know how that goes.

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 22, 2023, 2:44am UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/5 "2023-01-22T02:44:24Z")

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Forgot to add the command to start the server:

monailabel start\_server --app radiology\_full\_ct-upgraded-HYBRID/ --studies PATH\_TO\_IMAGES/ --conf models segmentation\_full\_ct

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 22, 2023, 6:51pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/6 "2023-01-22T18:51:15Z")

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Hi @diazandr3s

Thank you for your answer

> [@diazandr3s](#):
>
> Can you try the **localization\_vertebra** or **vertebra\_pipeline**? It should be under the list of Auto Segmentation models.

None of them worked, one gave an empty result and the other an error of mismatching tensor size on the server

> [@diazandr3s](#):
>
> monailabel start\_server --app radiology\_full\_ct-upgraded-HYBRID/ --studies PATH\_TO\_IMAGES/ --conf models segmentation\_full\_ct

This one worked. Thank you

 ![Captura desde 2023-01-22 14-30-25](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/d/fd6377955019558d68be2954dbff91096f00dc0f.jpeg)

The original CT had 0.65mm spacing, but the automatic segmentation result looks much rougher than when I do a manual threshold. Please see the picture below:

 ![Captura desde 2023-01-22 15-49-56](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/4/440467d90cd21c6380f58c13d955ad11a62e1bfe.jpeg)

Can this be corrected?

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [January 22, 2023, 7:05pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/7 "2023-01-22T19:05:20Z")

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Yes, this is expected - @diazandr3s has told me that this model is only trained at 1.5mm and another at 2mm which is the same as TotalSegmentator. In my experience the MONAI Label ct\_full and TotalSegmentator give comparable results, just with different resource requirements (MONAI can be faster but uses more memory). I understand either could be trained to run inference at higher resolution but I don’t believe that has happened yet. We plan to do some spine-specific higher resolution models with @Ron Alkalay.

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**Author:** ![Ron](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ron/32/10835_2.png) [@Ron](https://discourse.slicer.org/u/Ron)\
**Post date:** [January 22, 2023, 7:17pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/8 "2023-01-22T19:17:47Z")

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Thanks. flying out today, will have internet by 9 or 10 est tomorrow

Ron N Alkalay  
Associate Professor,  
Dept of Orthopedic Surgery, Harvard Medical School  
Center for Advanced  
Orthopedic Studies  
Beth Israel  
Deaconess Medical Center  
1 Overland Street  
Boston, MA, 02215  
Tel. 617-667-5185  
Fax. 617-667-7175  
email:  
rn\_alkalay@bidmc.harvard.edu

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 22, 2023, 9:14pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/9 "2023-01-22T21:14:23Z")

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Thanks for sharing the results, @mau_igna_06.

As @pieper said, we’ve trained two models on the Total Segmentator dataset: one using 1.5mm and the other using 2mm.

Just to check how it goes, could you try running inference after changing the **self.target\_spacing** values to (0.6, 0.6, 0.6) in the file _lib/configs/segmentation\_full\_ct_?

![Screenshot from 2023-01-22 21-09-11](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/8/5863a17b2f3e2bab57203d1a3900c7a3790d1837.png)

Retraining the model on better resolution shouldn’t be difficult at all. You just need to change the **self.target\_spacing** values to (0.6, 0.6, 0.6), or the one that fits on your GPU/CPU, in the file _lib/configs/segmentation\_full\_ct_ and trigger training.

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 22, 2023, 9:39pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/10 "2023-01-22T21:39:15Z")

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Hi @diazandr3s

Thank you for your answer

> [@diazandr3s](#):
>
> Just to check how it goes, could you try running inference after changing the **self.target\_spacing** values to (0.6, 0.6, 0.6) in the file _lib/configs/segmentation\_full\_ct_?

I’ll do

I wonder if we could train a preliminar stage of a bone segmentation model using just binary thresholds (then they could be separated by connected components by another stage or a human) or create an expert threshold limit chooser for bones segmentation using the training data from totalSegmentator.  
On our application, making anatomic surgical guide bases, only surface of cortical bone is important (considering other geometric restrictions). Currently we create them with the segment editor.

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 22, 2023, 9:46pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/11 "2023-01-22T21:46:14Z")

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Definitely! that can be done. This is a good question/topic to talk about during the workshop this Wednesday 🙂

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**Author:** ![mau\_igna\_06](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/mau_igna_06/32/9056_2.png) [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Post date:** [January 23, 2023, 5:00pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/12 "2023-01-23T17:00:27Z")

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Hi

> [@diazandr3s](#):
>
> Just to check how it goes, could you try running inference after changing the **self.target\_spacing** values to (0.6, 0.6, 0.6) in the file _lib/configs/segmentation\_full\_ct_?

My laptop could not allocate 58GB of RAM

Thank you anyway, I’ll keep exploring in the near future with better (cloud?) hardware

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**Author:** ![diazandr3s](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/diazandr3s/32/9973_2.png) [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Post date:** [January 23, 2023, 5:05pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243/13 "2023-01-23T17:05:58Z")

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I suspected this is the challenge with high-resolution images