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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: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:
      None

      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:
              marmaduke.woodman Marmaduke Woodman
              Reporter:
              paul.triebkorn Paul Triebkorn
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                Dates

                Created:
                Updated: