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  1. The Virtual Brain
  2. TVB-2808

shape mismatch in SpatialAverage monitors default spatial mask

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.4
    • Component/s: None
    • Labels:
      None
    • Epic Link:
    • Sprint:
      VBC Sprint 13
    • TVB-C Task:
      8.2 Pipeline Integration

      Description

      Running a surface simulation with subcortical regions in the connectome
      caused an error when using the SpatialAverage monitor together with the default spatial mask,
      i.e. this will default to the surface region map.
      This is not enough, because it ignores the subcortical regions and causes a shape mismatch
      when configuring the monitor.

      Traceback (most recent call last):
       File "/Users/pault/miniconda3/envs/tvb/lib/python3.7/multiprocessing/pool.py", line 121, in worker
       result = (True, func(*args, **kwds))
       File "/Users/pault/miniconda3/envs/tvb/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
       return list(map(*args))
       File "/Users/pault/Projects/neural_field_epileptor/SIMULATE.py", line 111, in run_one_epi_sim
       sim.configure()
       File "/Users/pault/miniconda3/envs/tvb/lib/python3.7/site-packages/tvb/simulator/simulator.py", line 288, in configure
       self._configure_monitors()
       File "/Users/pault/miniconda3/envs/tvb/lib/python3.7/site-packages/tvb/simulator/simulator.py", line 534, in _configure_monitors
       monitor.config_for_sim(self)
       File "/Users/pault/miniconda3/envs/tvb/lib/python3.7/site-packages/tvb/simulator/monitors.py", line 280, in config_for_sim
       raise Exception(msg)
      Exception: spatial_mask must be a vector of length number_of_nodes.
      

      Would it make sense to use the simulator._regmap attribute instead of simulator.surface.region_mapping,
      because the subcortical regions are included there ?
      In monitors.py on line 265.

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              Assignee:
              robert.vincze Robert Francisc Vincze
              Reporter:
              paul.triebkorn Paul Triebkorn
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                Dates

                Created:
                Updated:
                Resolved:

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