Hello, I am trying to create a montage and plot the electrodes for a dataset I have. The dataset is in .nwb format. I extracted the information from .nwb file into a pandas data frame and I am trying to create a montage following the tutorials. An error is raised when I try to align the electrodes …

I did manage to plot the electrodes . It was trivial, I just divided the coordinates with 1000. Thank you for the help. :grinning_face_with_smiling_eyes:

ping @alexrockhill and @adam2392 , they are most likely to be able to help with this.

Your electrodes are probably in coord_frame='mri_voxel' if you got them from a CT that was registered to the MRI. Also el_position has to be a dictionary with names and positions, not sure if that’s the case since it’s not in the code you shared but thought I’d mention it.

[image] JanevaD: montage = mne.channels.make_dig_montage( el_position, coord_frame='mri_voxel') might be more accurate. But now that I read your notes more carefully I see that everything looks in order as far as inputs. You don’t get any errors when you try to set the montage? Also you…

Sorry, this error kinda slipped trough my eyes. When I try to set the montage, when I execute the line of code raw.set_montage(montage) it raises a warning. RuntimeWarning: Fiducial point nasion not found, assuming identity unknown to head transformation And it also raises an error : TypeError…

Looks like there might have actually been an error in the first line causing your montage to be None as well. From the error, it appears as though you’re trying to set a NoneType montage as the montage. So I would check the first line and maybe also plot the montage when you make it. (montage.plot())…

The montage type is channel.montage.DigMontage and I did plot it, it is right. When I run raw.set_montage(montage) I get this in the console: In[12]: raw.set_montage(montage) <ipython-input-12-1eda6b6b16a2>:1: RuntimeWarning: Fiducial point nasion not found, assuming identity unknown to head tran…

that error can be ignored and should only happen within Jupyter Notebook and maybe Jupyter Lab. It’s related to the way we do fancy printing of the Raw object in HTML contexts. The bug has already been reported here: filename issue with the new _repr_html_ when creating RawArray directly · Issue #…

I see, thank you. I am sill unable to plot the alignment of the electrodes. It doesn’t raise any kind of error. Only the brain mri is shown in pyVista, without aligned electrodes.

Does the montage plot without anything else?

[image] JanevaD: I am sill unable to plot the alignment of the electrodes. It doesn’t raise any kind of error. Only the brain mri is shown in pyVista, without aligned electrodes. I wonder if you’re encountering the same problem in this thread ? We’ve had trouble replicating the problem in tha…

Trouble plotting EcoG electrodes

Support & Discussions

drammock (Dan McCloy) May 14, 2021, 9:58pm 11

I wonder if you’re encountering the same problem in this thread? We’ve had trouble replicating the problem in that thread… if it’s the same issue it would be helpful to know that you’re seeing it in Linux Mint too (the other user is on a mac). cc @larsoner

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Trouble plotting EcoG electrodes

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