Inquiry about error in tutorial_s5_ModelingRestingStateNetworks.ipynb

[Chuyue Zhao]

Dear TVB Team,

I am learning to use TVB for brain network simulations. While running your tutorial file tutorial_s5_ModelingRestingStateNetworks.ipynb, I encountered the following issue:

When I execute:

for reg in 'lM1 rPFCVL rPCS'.split():
    plot_roi_corr_map(reg)

I get this error:

TraitAttributeError                       Traceback (most recent call last)
Cell In[8], line 2
      1 for reg in 'lM1 rPFCVL rPCS'.split():
----> 2     plot_roi_corr_map(reg)

Cell In[7], line 4
      2 roi = list(conn.ordered_labels).index(reg_name)
      3 cs_m = cs[2:].mean(axis=0)
----> 4 rm = utils.cortex.region_mapping
      5 utils.multiview(cs_m[roi][rm], shaded=False, suptitle=reg_name, figsize=(10, 5))

File c:\Users\MSI-NB\miniconda3\envs\tvb\Lib\site-packages\tvb\datatypes\cortex.py:70, in Cortex.region_mapping(self)
     68     return self._regmap
     69 rm = self.region_mapping_data.array_data
---> 70 unmapped = self.region_mapping_data.connectivity.unmapped_indices(rm)
     71 self._regmap = numpy.r_[rm, unmapped]
     72 return self._regmap

File c:\Users\MSI-NB\miniconda3\envs\tvb\Lib\site-packages\tvb\basic\neotraits\_attr.py:164, in Attr.__get__(self, instance, owner)
    162 value = instance.__dict__[self.field_name]
    163 if self.required and value is None:
--> 164     raise TraitAttributeError('required attribute referenced before assignment. '
    165                               'Use a default or assign a value before reading it', attr=self)
    166 return value

TraitAttributeError: required attribute referenced before assignment. Use a default or assign a value before reading it

  attribute tvb.datatypes.region_mapping.RegionMapping.connectivity = Attr(field_type=<class 'tvb.datatypes.connectivity.Connectivity'>, default=None, required=True).

From the traceback, it appears that cortex.region_mapping is being accessed before the region_mapping_data.connectivity attribute is properly initialized. I suspect I need to assign a valid Connectivity object to ctx.region_mapping_data.connectivity (or load it from a file), but I'm not entirely sure how to do this correctly for this tutorial.

Could you please advise me on the proper steps or configuration needed to resolve this error? Any guidance or reference to relevant documentation would be greatly appreciated.

Thank you very much for your time and support.

Sincerely,
Chuyue

[WOODMAN Michael]

Hi,

Here’s an example notebook you can work from

https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/demos/simulate_surface_seeg_eeg_meg.ipynb

cheers,

Marmaduke

On 19 Jan 2025, at 05:31, Chuyue Zhao <zhaoch...@gmail.com> wrote:

Ce mail provient de l'extérieur, restons vigilants

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[Chuyue Zhao]

Hi Marmaduke,
Thank you for your reply and the provided notebook, I'll try it.

Best,

Chuyue

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