Describe the bug
Uploading my own T1-CE .nii and performing pre-operative segmentation yields an error "No radiological volume for {'timestamp': 0, 'sequence': 'T1-CE', 'labels': None, 'space': {'timestamp': 0, 'sequence': 'T1-CE'}}" even after manually setting the sequence type to T1-CE. This behaviour does not appear with the approved example data.
Computer settings:
- Operating System : Windows 11
- Processor (CPU) type: AMD Ryzen
To Reproduce
- Go to "Import patient"
- Click on "Other data type (*.nii)
- Open T1-CE .nii
- Set sequence type to T1-CE in dropdown
- Go to "Actions" and then start pre-operative segmentation
Error messages
Note -- filename anonymized in error output below
DEBUG:root:New patient creation requested.
INFO:root:Output patient directory set to: C:\Users\frede.raidionics\patients\temp_patient
INFO:root:Renamed current output folder to: C:\Users\frede.raidionics\patients\melody_montano
DEBUG:root:Active patient uid changed from None to 84275.
DEBUG:root:Loading patient 84275 from memory.
INFO:root:New data file imported: 7065_02216760_2019-06-13_ANON_t1_vibe_tra_p2_FS_STRAIGHT
DEBUG:root:Unsaved changes - Patient object expanded with new volumes.
INFO:root:[MRISeriesLayerWidget] Visibility toggled to True for 7065_02216760_2019-06-13_ANON_t1_vibe_tra_p2_FS_STRAIGHT
DEBUG:root:Unsaved changes - MRI volume sequence changed to T1-CE
INFO:root:Starting pipeline process for task: preop_segmentation.
INFO:root:Starting pipeline process for patient 84275 and task preop_segmentation.
INFO:root:Saving patient results in: C:\Users\frede.raidionics\patients\melody_montano
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): github.com:443
DEBUG:urllib3.connectionpool:https://github.com:443 "GET /raidionics/Raidionics-models/releases/download/1.2.0/raidionics_cloud_models_list_github.csv HTTP/1.1" 302 0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): objects.githubusercontent.com:443
DEBUG:urllib3.connectionpool:https://objects.githubusercontent.com:443 "GET /github-production-release-asset-2e65be/601122702/e623363f-d633-4134-ad39-0a9a03cdbd92?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20240229%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240229T065226Z&X-Amz-Expires=300&X-Amz-Signature=aefbb8d3a2372378dbf32dbc8ca1e6800d641146b8cd16eaea3dfd43cf0dd3b4&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=601122702&response-content-disposition=attachment%3B%20filename%3Draidionics_cloud_models_list_github.csv&response-content-type=application%2Foctet-stream HTTP/1.1" 200 1754
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): github.com:443
DEBUG:urllib3.connectionpool:https://github.com:443 "GET /raidionics/Raidionics-models/releases/download/1.2.0/raidionics_cloud_models_list_github.csv HTTP/1.1" 302 0
DEBUG:urllib3.connectionpool:Starting new HTTPS connection (1): objects.githubusercontent.com:443
DEBUG:urllib3.connectionpool:https://objects.githubusercontent.com:443 "GET /github-production-release-asset-2e65be/601122702/e623363f-d633-4134-ad39-0a9a03cdbd92?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20240229%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20240229T065226Z&X-Amz-Expires=300&X-Amz-Signature=aefbb8d3a2372378dbf32dbc8ca1e6800d641146b8cd16eaea3dfd43cf0dd3b4&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=601122702&response-content-disposition=attachment%3B%20filename%3Draidionics_cloud_models_list_github.csv&response-content-type=application%2Foctet-stream HTTP/1.1" 200 1754
C:\Users\frede\anaconda3\Lib\site-packages\paramiko\transport.py:219: CryptographyDeprecationWarning: Blowfish has been deprecated
"class": algorithms.Blowfish,
ERROR:root:Pipeline process for patient 84275, for task preop_segmentation failed with:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\Pipelines\SegmentationStep.py", line 71, in setup
raise ValueError("No radiological volume for {}.".format(input_json))
ValueError: No radiological volume for {'timestamp': 0, 'sequence': 'T1-CE', 'labels': None, 'space': {'timestamp': 0, 'sequence': 'T1-CE'}}.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\frede\anaconda3\Lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "C:\Research\fgs\segmentation\raidionics\Raidionics-master\utils\backend_logic.py", line 187, in run_pipeline_wrapper
run_rads(params[0], params[1])
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\compute.py", line 30, in run_rads
patient_parameters = pip.execute(patient_parameters=patient_parameters)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\Pipelines\PipelineStructure.py", line 90, in execute
self._steps[s].setup(patient_parameters)
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\Pipelines\SegmentationStep.py", line 147, in setup
raise ValueError("[SegmentationStep] setup failed.")
ValueError: [SegmentationStep] setup failed.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:\Research\fgs\segmentation\raidionics\Raidionics-master\utils\backend_logic.py", line 126, in run_pipeline
ret = result.get()[0]
^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\multiprocessing\pool.py", line 774, in get
raise self._value
File "C:\Users\frede\anaconda3\Lib\multiprocessing\pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\multiprocessing\pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^^
File "C:\Research\fgs\segmentation\raidionics\Raidionics-master\utils\backend_logic.py", line 187, in run_pipeline_wrapper
run_rads(params[0], params[1])
^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\compute.py", line 30, in run_rads
patient_parameters = pip.execute(patient_parameters=patient_parameters)
^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\Pipelines\PipelineStructure.py", line 90, in execute
self._steps[s].setup(patient_parameters)
^^^^^^^^^^^^^^^^^
File "C:\Users\frede\anaconda3\Lib\site-packages\raidionicsrads\Pipelines\SegmentationStep.py", line 147, in setup
raise ValueError("[SegmentationStep] setup failed.")
^^^^^^^^^^^^^^^^^
ValueError: [SegmentationStep] setup failed.
INFO:root:Saving patient results in: C:\Users\frede.raidionics\patients\melody_montano
Any assistance would be greatly appreciated!