Adding support for Nicolet .e files

[MureziCapaul]

There is currently no support for .e files produced by NicoletOne systems (now aquired by Natus).
Is anyone working on adding support for these files? If not, I will give it a try. The hospital I work in has .e files reaching about a decade back, and it would be great if these were easily available for research.

There already exists a reader in MATLAB (https://github.com/ieeg-portal/Nicolet-Reader), which I will use as a starting point.
If anyone has more information on this particular filetype, it would be greatly appreciated.

[zm711]

@MureziCapaul,

I've never heard of that format and I can say that no one is working on it. Feel free to give it a go and then we can review it when done. Our documentation goes over making a new RawIO and then we have functions to automatically convert it to an IO. See our example rawio for help working on the rawio.

[MureziCapaul]

Thanks for your response, given my other duties at work it will probably take a few weeks until I have a working version, and then I will come back at you.
Best,
Muri

[MureziCapaul]

Hi @zm711 ,

It's been a long time, but I have now finished a version of the IO-Module that passes all the required tests, and I would now like to add it to the Neo Library. I pushed it to my fork of the Neo-Repository
I have also opened an issue on the ephys data repository to add my test file to the repository.

You also seem to have added some workflows now that every push to the repository needs to pass. They ran on my Neo fork.

• 'NeoCoreTest' passed.
• 'Mirror to EBRAINS' resulted in an authentication error.
  remote: HTTP Basic: Access denied. The provided password or token is incorrect or your account has 2FA enabled and you must use a personal access token instead of a password
  According to this: https://gitlab.ebrains.eu/help/user/profile/account/two_factor_authentication_troubleshooting.md , I need to use a personal access token. Where would I add this?
• 'NeoIOTest-automatic-trigger' and 'Create cashes for ephys training data' had been running for about an hour, and I decided to cancel them. Do they not work when I have not yet added my training data to the ephys repository?

Best,
Muri

[zm711]

Howdy @MureziCapaul !

I have also opened an issue on the ephys data repository to add my test file to the repository.

So we can review your test dataset shortly and add that to gin. You shouldn't need an issue open you should be able to do a PR. If you don't want to submit the file yourself the best thing you can do is share it here on github so we can download it and then put it into the repo ourselves. I'll double check testing repo to confirm what is happening.

you also seem to have added some workflows now that every push to the repository needs to pass. They ran on my Neo fork.

This is actually not our thing. This is a github thing. They do this in case you decide to try to make your own private version of neo you'll still be able to run the tests. We actually recommend shutting that off to be environmentally friendly. Once you try to submit your PR here on the main repo we will run the official tests and those are the ones that need to pass. They only take about 10 minutes, so it likely means something isn't set up correctly on your repo for the test. Again you do not need to spend the time to set it up correctly unless you want to.

The next step for you is to open an official PR here.

To open the PR follow the above three steps. You'll submit the PR and then we can review it. Since the testing files are not submitted yet the tests will fail. They will only work once we have the testing file merged to our other repo. Let me know if you have any questions about that! I'll check the ephy repo now and comment over there for the file.
Zach

[MureziCapaul]

Hi @zm711 ,

Thanks a lot. Here's a link to the test file: https://share.swissepi.ch/link/VKJTNOCotCKy2fpK3l2CD2 .
I will open the pull request next monday.

Have a good weekend,
Muri

[zm711]

@MureziCapaul a couple of us tried to access your file and we couldn't access it. It is saying the site can't be reached. Could you try sharing another way.

[MureziCapaul]

@zm711 That's weird. Anyway, here's a google drive link, that should work:
https://drive.google.com/file/d/1T4aKlUmg_sy7xfutxgVwg7uClvTxNu4a/view?usp=sharing

[zm711]

That seems to have worked! Last thing we need is the provenance. Typically something like:

4 channels of data recorded on Nicolet version 3 in lab of xx. Should have eeg, stimulus data.