MNE dipole simulator doesn't open

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1

Hi @richard I have been trying to run MNE dipole simulator for two days now, but the program takes too long to start up and ends up giving me server error. Not just me, everyone in my lab has been facing this problem. Has the deploying server changed or is it an issue on part of MNE?

Found built image, launching...
Launching server...
Server requested
2022-06-16T18:46:59Z [Normal] Successfully assigned bhub-ns/jupyter-mne-2dtools-2ddipole-2dsimulator-2d682g8a5b to spko-css-app03
2022-06-16T18:46:36Z [Normal] Created container block-cloud-metadata
2022-06-16T18:46:36Z [Normal] Started container block-cloud-metadata
2022-06-16T18:46:59Z [Normal] Successfully assigned bhub-ns/jupyter-mne-2dtools-2ddipole-2dsimulator-2d682g8a5b to spko-css-app03
2022-06-16T18:46:37Z [Normal] Created container notebook
2022-06-16T18:46:37Z [Normal] Started container notebook
2022-06-16T18:46:59Z [Normal] Successfully assigned bhub-ns/jupyter-mne-2dtools-2ddipole-2dsimulator-2d682g8a5b to spko-css-app03
Server ready at /binder/jupyter/user/mne-tools-dipole-simulator-682g8a5b/
server running at https://notebooks.gesis.org/binder/jupyter/user/mne-tools-dipole-simulator-682g8a5b/

And it ends like this

There was an error when executing cell [2]. Please run VoilĂ  with --show_tracebacks=True or --debug to see the error message, or configure VoilaConfiguration.show_tracebacks.
2

Hello, I had the same problem when I checked a few days ago and had hoped it was just a temporary disturbance. Seems that was not the case … I’ll try to look into this tomorrow. Please ping me again if you don’t hear back from me within the next few days.

2 Likes
3

Hello, I fixed the simulator and you can now use it again at

1 Like
4

Hi @richard,

The dipole simulator doesn’t let me change the slices as per my own (only lets me use the preset) nor helps me see the topography. Is it the issue with the simulator or am I not understanding how the simulator works?

image
image740Ă—899 62.3 KB

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Hello @Rekha, the browser window shown in your screenshot seems unusually narrow, and apparently, this is breaking the layout. Can you make the window wider? You’re supposed to see 3 slices (3 different planes) aligned right next to each other in a single row…

Screen Shot 2022-06-26 at 20.48.29
Screen Shot 2022-06-26 at 20.48.292242Ă—1722 334 KB

6

The index page turns out to be blank most of the times I reload the simulator and when I try extending the window, the simulator gets stuck.

For example:

This is he index page most of the times. I continuously have to refresh it

image
image1203Ă—937 15 KB

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When I try extending the window, this is what i get

image
image1825Ă—850 178 KB

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I can reproduce the problem with Chrome:

Screen Shot 2022-06-26 at 21.23.46
Screen Shot 2022-06-26 at 21.23.462784Ă—1712 272 KB

I’d only tested with Safari recently, where it works just fine.

If you have access to Safari, try this. I think it even worked on my iPad for me the last time I checked.

1 Like
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Hi @richard, it worked on safari. One more question: are the coordinates in MRI , or MNI coordinates system? And can we upload our own MRI or can only work with the template in the simulator?

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I found out this is a problem with the mybinder website.

If you clone the repository, create a new conda environment based on the dependencies listed in environment.html, and run this thing via voila, all works fine, even in Chrome.

1 Like
12

thanks @richard,Please let me know if you whether the x,y,z coordinates in the dipole simulator are in MNI or SCS format.

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I believe the coordinates are in scanner RAS, but I’d have to check. There is currently no support for custom images.