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  1. The Virtual Brain
  2. TVB-3040

Siibra creator not working with other atlas than default

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Details

    • Bug
    • Status: Resolved
    • Critical
    • Resolution: Fixed
    • 2.7
    • 2.7
    • None
    • VBC Sprint 14

    Description

      2022-11-04 10:31:27,454 - WARNING [proc:98884]  - siibra - This is a development release. Use at your own risk.
      2022-11-04 10:31:27,454 - INFO [proc:98884]  - siibra - Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.
      2022-11-04 10:31:28,514 - INFO [proc:98884]  - tvb.adapters.creators.siibra_base - Using atlas Allen Mouse Common Coordinate Framework v3 and parcellation Allen Mouse Common Coordinate Framework v3 2017
      2022-11-04 10:31:28,514 - INFO [proc:98884]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:31:34,374 - ERROR [proc:98884]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.WEIGHTS were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:31:34,375 - INFO [proc:98884]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:31:34,873 - ERROR [proc:98884]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.TRACTS were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:31:34,873 - ERROR [proc:98884]  - tvb.adapters.creators.siibra_base - Could not find both weights and tract lengths from parcellation Allen Mouse Common Coordinate Framework v3 2017, so a connectivity cannot be computed
      2022-11-04 10:31:34,873 - INFO [proc:98884]  - tvb.adapters.creators.siibra_base - Using atlas Allen Mouse Common Coordinate Framework v3 and parcellation Allen Mouse Common Coordinate Framework v3 2017
      2022-11-04 10:31:34,873 - INFO [proc:98884]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:31:35,379 - ERROR [proc:98884]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.FC were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:31:35,379 - ERROR [proc:98884]  - tvb.adapters.creators.siibra_base - Could not find any functional connectivity in parcellation Allen Mouse Common Coordinate Framework v3 2017, so a TVB Functional Connectivity cannot be computed
      2022-11-04 10:31:35,379 - ERROR [proc:98884]  - tvb.core.services.operation_service - Could not launch Operation with the given input data!
      Traceback (most recent call last):
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 243, in initiate_prelaunch
          result_msg, nr_datatypes = adapter_instance._prelaunch(operation, view_model, available_space)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 90, in new_function
          return func(*args, **kw)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 353, in _prelaunch
          result = self.launch(view_model)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/adapters/creators/siibra_creator.py", line 190, in launch
          for subject_id, conn in conn_dict.items():
      AttributeError: 'NoneType' object has no attribute 'items'
      2022-11-04 10:31:35,408 - ERROR [proc:98884]  - tvb.core.operation_async_launcher - Could not execute operation 15
      2022-11-04 10:31:35,408 - ERROR [proc:98884]  - tvb.core.operation_async_launcher - 'NoneType' object has no attribute 'items'
      Traceback (most recent call last):
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/operation_async_launcher.py", line 79, in do_operation_launch
          OperationService().initiate_prelaunch(curent_operation, adapter_instance)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 262, in initiate_prelaunch
          self._handle_exception(excep1, temp_files, msg, operation)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 319, in _handle_exception
          raise exception.with_traceback(
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 243, in initiate_prelaunch
          result_msg, nr_datatypes = adapter_instance._prelaunch(operation, view_model, available_space)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 90, in new_function
          return func(*args, **kw)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 353, in _prelaunch
          result = self.launch(view_model)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/adapters/creators/siibra_creator.py", line 190, in launch
          for subject_id, conn in conn_dict.items():
      AttributeError: 'NoneType' object has no attribute 'items'
      2022-11-04 10:32:22,358 - INFO [proc:98979]  - siibra - Version: 0.3a27
      2022-11-04 10:32:22,358 - WARNING [proc:98979]  - siibra - This is a development release. Use at your own risk.
      2022-11-04 10:32:22,358 - INFO [proc:98979]  - siibra - Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.
      2022-11-04 10:32:23,260 - INFO [proc:98979]  - tvb.adapters.creators.siibra_base - Using atlas Allen Mouse Common Coordinate Framework v3 and parcellation Allen Mouse Common Coordinate Framework v3 2017
      2022-11-04 10:32:23,260 - INFO [proc:98979]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:32:25,982 - ERROR [proc:98979]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.WEIGHTS were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:32:25,982 - INFO [proc:98979]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:32:26,912 - ERROR [proc:98979]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.TRACTS were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:32:26,913 - ERROR [proc:98979]  - tvb.adapters.creators.siibra_base - Could not find both weights and tract lengths from parcellation Allen Mouse Common Coordinate Framework v3 2017, so a connectivity cannot be computed
      2022-11-04 10:32:26,913 - INFO [proc:98979]  - tvb.adapters.creators.siibra_base - Using atlas Allen Mouse Common Coordinate Framework v3 and parcellation Allen Mouse Common Coordinate Framework v3 2017
      2022-11-04 10:32:26,913 - INFO [proc:98979]  - siibra - Found 2 versions for dataset 'Parcellation-based structural and resting-state functional brain connectomes of a healthy cohort' (v1.0, v1.1). Will use v1.1 per default.
      2022-11-04 10:32:27,517 - ERROR [proc:98979]  - tvb.adapters.creators.siibra_base - No connectivity Component2Modality.FC were found in parcellation Allen Mouse Common Coordinate Framework v3 2017!
      2022-11-04 10:32:27,517 - ERROR [proc:98979]  - tvb.adapters.creators.siibra_base - Could not find any functional connectivity in parcellation Allen Mouse Common Coordinate Framework v3 2017, so a TVB Functional Connectivity cannot be computed
      2022-11-04 10:32:27,517 - ERROR [proc:98979]  - tvb.core.services.operation_service - Could not launch Operation with the given input data!
      Traceback (most recent call last):
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 243, in initiate_prelaunch
          result_msg, nr_datatypes = adapter_instance._prelaunch(operation, view_model, available_space)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 90, in new_function
          return func(*args, **kw)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 353, in _prelaunch
          result = self.launch(view_model)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/adapters/creators/siibra_creator.py", line 190, in launch
          for subject_id, conn in conn_dict.items():
      AttributeError: 'NoneType' object has no attribute 'items'
      2022-11-04 10:32:27,545 - ERROR [proc:98979]  - tvb.core.operation_async_launcher - Could not execute operation 16
      2022-11-04 10:32:27,545 - ERROR [proc:98979]  - tvb.core.operation_async_launcher - 'NoneType' object has no attribute 'items'
      Traceback (most recent call last):
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/operation_async_launcher.py", line 79, in do_operation_launch
          OperationService().initiate_prelaunch(curent_operation, adapter_instance)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 262, in initiate_prelaunch
          self._handle_exception(excep1, temp_files, msg, operation)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 319, in _handle_exception
          raise exception.with_traceback(
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/services/operation_service.py", line 243, in initiate_prelaunch
          result_msg, nr_datatypes = adapter_instance._prelaunch(operation, view_model, available_space)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 90, in new_function
          return func(*args, **kw)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/core/adapters/abcadapter.py", line 353, in _prelaunch
          result = self.launch(view_model)
        File "/Users/lia.domide/WORK/TVB/root-git/tvb-root/tvb_framework/tvb/adapters/creators/siibra_creator.py", line 190, in launch
          for subject_id, conn in conn_dict.items():
      AttributeError: 'NoneType' object has no attribute 'items'
      

      In web GUI, we get the AttributeError message 'NoneType' object has no attribute 'items', and at least we should get the custom message: "No connectivity found..."

      Also, if no other atlas then the default has compatible data, maybe we shouldn't show all options

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              romina.baila Romina Baila
              lia.domide Lia Domide
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                Updated:
                Resolved:

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