Saving Monailabel Segmentations to Orthanc #1820

soumen02 · 2025-03-14T09:36:20Z

soumen02
Mar 14, 2025

Hello,

I am testing out MonaiLabel with OHIF/Orthanc. The segmentation is working but I'm unable to figure out how to save the labels back to Orthanc as Dicom-Seg. Is there a good way to do this already or do I have to figure out a workaround.

Logs

[2025-03-14 13:17:58,341] [352495] [MainThread] [INFO] (monailabel.transform.writer:196) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2025-03-14 13:17:58,469] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:335) - ++ Latencies => Total: 3.1729; Pre: 0.5279; Inferer: 0.6096; Invert: 0.0170; Post: 1.8891; Write: 0.1285
[2025-03-14 13:17:58,470] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:370) - Result File: /tmp/tmphsspi58x.nrrd
[2025-03-14 13:17:58,470] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:371) - Result Json Keys: ['label_names', 'latencies', 'centroids']
[2025-03-14 13:19:01,486] [352495] [MainThread] [INFO] (monailabel.endpoints.infer:169) - Infer Request: {'model': 'segmentation', 'image': '1.3.6.1.4.1.34261.345051866108.7484.1646883116.0', 'label_prompt': [5], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False}
[2025-03-14 13:19:01,487] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:78) - Image ID: 1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:19:01,487] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:80) - Image Dir (cache): /home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:19:01,487] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:280) - Infer Request (final): {'largest_cc': False, 'device': 'cuda:0', 'model': 'segmentation', 'image': '/home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0.nii.gz', 'label_prompt': [5], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False, 'description': 'A pre-trained model for volumetric (3D) Segmentation from CT image'}
[2025-03-14 13:19:01,488] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2025-03-14 13:19:01,488] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path']
[2025-03-14 13:19:01,968] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (LoadImaged): Time: 0.4798; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:19:01,984] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureTyped): Time: 0.0151; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:19:01,984] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureChannelFirstd): Time: 0.0002; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:19:01,985] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Orientationd): Time: 0.0011; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:19:01,989] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Spacingd): Time: 0.0035; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:01,993] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (NormalizeIntensityd): Time: 0.0038; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:01,995] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (GaussianSmoothd): Time: 0.0016; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:02,000] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityd): Time: 0.005; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:02,000] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:503) - Inferer:: cuda:0 => 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, 'buffer_steps': None, 'buffer_dim': -1, 'with_coord': False, 'roi_weight_map': None}
[2025-03-14 13:19:02,000] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:432) - Infer model path: /home/sm8966/radiology/model/pretrained_segmentation.pt
[2025-03-14 13:19:02,616] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - INV - Run Transform(s)
[2025-03-14 13:19:02,616] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - INV - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:19:02,625] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Spacingd): Time: 0.0083; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:02,626] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Orientationd): Time: 0.001; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:19:02,626] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - POST - Run Transform(s)
[2025-03-14 13:19:02,626] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - POST - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:19:02,627] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (EnsureTyped): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:19:02,627] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Activationsd): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:19:02,627] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (AsDiscreted): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:19:02,627] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Restored): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:19:04,483] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (GetCentroidsd): Time: 1.8556; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:19:04,483] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:603) - Writing Result...
[2025-03-14 13:19:04,484] [352495] [MainThread] [INFO] (monailabel.transform.writer:196) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2025-03-14 13:19:04,607] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:335) - ++ Latencies => Total: 3.1203; Pre: 0.5122; Inferer: 0.6149; Invert: 0.0113; Post: 1.8574; Write: 0.1240
[2025-03-14 13:19:04,608] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:370) - Result File: /tmp/tmplo0mizw8.nrrd
[2025-03-14 13:19:04,608] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:371) - Result Json Keys: ['label_names', 'latencies', 'centroids']
[2025-03-14 13:20:19,986] [352495] [MainThread] [INFO] (monailabel.endpoints.infer:169) - Infer Request: {'model': 'segmentation', 'image': '1.3.6.1.4.1.34261.345051866108.7484.1646883116.0', 'label_prompt': [3, 2], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False}
[2025-03-14 13:20:19,987] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:78) - Image ID: 1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:20:19,987] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:80) - Image Dir (cache): /home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:20:19,988] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:280) - Infer Request (final): {'largest_cc': False, 'device': 'cuda:0', 'model': 'segmentation', 'image': '/home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0.nii.gz', 'label_prompt': [3, 2], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False, 'description': 'A pre-trained model for volumetric (3D) Segmentation from CT image'}
[2025-03-14 13:20:19,989] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2025-03-14 13:20:19,989] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path']
[2025-03-14 13:20:20,470] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (LoadImaged): Time: 0.481; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:20,486] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureTyped): Time: 0.0153; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:20,486] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureChannelFirstd): Time: 0.0002; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:20,488] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Orientationd): Time: 0.0014; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:20,491] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Spacingd): Time: 0.0035; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:20,495] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (NormalizeIntensityd): Time: 0.0038; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:20,497] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (GaussianSmoothd): Time: 0.0016; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:20,502] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityd): Time: 0.0051; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:20,502] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:503) - Inferer:: cuda:0 => 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, 'buffer_steps': None, 'buffer_dim': -1, 'with_coord': False, 'roi_weight_map': None}
[2025-03-14 13:20:20,502] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:432) - Infer model path: /home/sm8966/radiology/model/pretrained_segmentation.pt
[2025-03-14 13:20:21,114] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - INV - Run Transform(s)
[2025-03-14 13:20:21,114] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - INV - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:20:21,122] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Spacingd): Time: 0.0082; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:21,123] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Orientationd): Time: 0.001; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:21,124] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - POST - Run Transform(s)
[2025-03-14 13:20:21,124] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - POST - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:20:21,124] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (EnsureTyped): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:21,124] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Activationsd): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:21,125] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (AsDiscreted): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:21,125] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Restored): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:22,998] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (GetCentroidsd): Time: 1.8724; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:22,998] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:603) - Writing Result...
[2025-03-14 13:20:22,998] [352495] [MainThread] [INFO] (monailabel.transform.writer:196) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2025-03-14 13:20:23,120] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:335) - ++ Latencies => Total: 3.1332; Pre: 0.5142; Inferer: 0.6100; Invert: 0.0114; Post: 1.8743; Write: 0.1225
[2025-03-14 13:20:23,121] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:370) - Result File: /tmp/tmp2vq8palh.nrrd
[2025-03-14 13:20:23,121] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:371) - Result Json Keys: ['label_names', 'latencies', 'centroids']
[2025-03-14 13:20:49,292] [352495] [MainThread] [INFO] (monailabel.endpoints.infer:169) - Infer Request: {'model': 'segmentation', 'image': '1.3.6.1.4.1.34261.345051866108.7484.1646883116.0', 'label_prompt': [3, 2, 5, 10, 6], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False}
[2025-03-14 13:20:49,293] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:78) - Image ID: 1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:20:49,293] [352495] [MainThread] [INFO] (monailabel.datastore.dicom:80) - Image Dir (cache): /home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0
[2025-03-14 13:20:49,294] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:280) - Infer Request (final): {'largest_cc': False, 'device': 'cuda:0', 'model': 'segmentation', 'image': '/home/sm8966/.cache/monailabel/dicom/488fca1f7f3f98331f6f7756beca0d35/1.3.6.1.4.1.34261.345051866108.7484.1646883116.0.nii.gz', 'label_prompt': [3, 2, 5, 10, 6], 'result_extension': '.nrrd', 'result_dtype': 'uint8', 'result_compress': False, 'restore_label_idx': False, 'description': 'A pre-trained model for volumetric (3D) Segmentation from CT image'}
[2025-03-14 13:20:49,294] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - PRE - Run Transform(s)
[2025-03-14 13:20:49,294] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - PRE - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path']
[2025-03-14 13:20:49,773] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (LoadImaged): Time: 0.4785; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:49,789] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureTyped): Time: 0.0162; image: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:49,790] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (EnsureChannelFirstd): Time: 0.0002; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:49,791] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Orientationd): Time: 0.0012; image: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:49,795] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (Spacingd): Time: 0.0035; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:49,799] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (NormalizeIntensityd): Time: 0.0037; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:49,800] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (GaussianSmoothd): Time: 0.0015; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:49,805] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - PRE - Transform (ScaleIntensityd): Time: 0.005; image: torch.Size([1, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:49,806] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:503) - Inferer:: cuda:0 => 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, 'buffer_steps': None, 'buffer_dim': -1, 'with_coord': False, 'roi_weight_map': None}
[2025-03-14 13:20:49,806] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:432) - Infer model path: /home/sm8966/radiology/model/pretrained_segmentation.pt
[2025-03-14 13:20:50,413] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - INV - Run Transform(s)
[2025-03-14 13:20:50,413] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - INV - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:20:50,422] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Spacingd): Time: 0.0084; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:50,423] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - INV - Transform (Orientationd): Time: 0.0011; image: torch.Size([26, 424, 346, 193])(torch.float32); pred: torch.Size([26, 224, 183, 129])(torch.float32)
[2025-03-14 13:20:50,424] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:76) - POST - Run Transform(s)
[2025-03-14 13:20:50,424] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:77) - POST - Input Keys: ['largest_cc', 'device', 'model', 'image', 'label_prompt', 'result_extension', 'result_dtype', 'result_compress', 'restore_label_idx', 'description', 'image_path', 'latencies', 'pred']
[2025-03-14 13:20:50,424] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (EnsureTyped): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:50,424] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Activationsd): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([26, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:50,425] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (AsDiscreted): Time: 0.0002; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([1, 424, 346, 193])(torch.float32)
[2025-03-14 13:20:50,425] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (Restored): Time: 0.0001; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:52,286] [352495] [MainThread] [INFO] (monailabel.interfaces.utils.transform:122) - POST - Transform (GetCentroidsd): Time: 1.8608; image: torch.Size([1, 224, 183, 129])(torch.float32); pred: torch.Size([424, 346, 193])(torch.float32)
[2025-03-14 13:20:52,286] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:603) - Writing Result...
[2025-03-14 13:20:52,287] [352495] [MainThread] [INFO] (monailabel.transform.writer:196) - Result ext: .nrrd; write_to_file: True; dtype: uint8
[2025-03-14 13:20:52,410] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:335) - ++ Latencies => Total: 3.1165; Pre: 0.5119; Inferer: 0.6058; Invert: 0.0119; Post: 1.8630; Write: 0.1235
[2025-03-14 13:20:52,410] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:370) - Result File: /tmp/tmph4zifnwc.nrrd
[2025-03-14 13:20:52,410] [352495] [MainThread] [INFO] (monailabel.tasks.infer.basic_infer:371) - Result Json Keys: ['label_names', 'latencies', 'centroids']

Appreciate the help,

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Saving Monailabel Segmentations to Orthanc #1820

Uh oh!

{{title}}

Uh oh!

Uh oh!

{{editor}}'s edit

{{editor}}'s edit

Uh oh!

Replies: 0 comments

Select a reply

Uh oh!

Saving Monailabel Segmentations to Orthanc #1820

Uh oh!

Uh oh!

soumen02 Mar 14, 2025

Replies: 0 comments

soumen02
Mar 14, 2025