[Mne_analysis] Topomap with Brainvision EEG data

Mon Nov 3 19:30:34 EST 2014

Hi Denis,
Thanks so much.This is very helpful!
Best,
Lakshmi
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Denis-Alexander Engemann [denis.engemann at gmail.com]
Sent: Monday, November 03, 2014 12:36 PM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Topomap with Brainvision EEG data

Dear Lakshmi,

sorry for the delay. I just completed your example to make it work. Let me know whether it makes you happy.

To recap, the problem was not the data or the topos themselves but the positioning of the sensors.
The solution is to first put the data in an mne container, mne.EvokedArrat in this case.
Then calling the high level viz functions / methods then does the trick, they will do some automatic rescaling of the sensor positions to match the outline definition, a head scheme in this case.

Here's the script.

https://gist.github.com/dengemann/dfa01ebd8c14a2316477

Here's EEG lab with non-sense data:
https://www.dropbox.com/s/7vs4hdp263hetmb/matlab_topomap.png?dl=0

Here MNE with non-sense data (from the example):
https://www.dropbox.com/s/ds7g667t3ih63c4/Screenshot%202014-11-03%2018.23.12.png?dl=0

Note. You'll need the development version of MNE tor run the code. It relies on the montage functionality that we have just added last Friday.

I hope this helps,
best,
Denis

2014-10-31 13:17 GMT+01:00 Lakshmi Krishnan <lakshmik at umd.edu<mailto:lakshmik at umd.edu>>:
Hi Denis,
I was hesitant to use real data since the electrode locations didn't match.
I read the brain vision eeg files into mne-python using mne.io.read_raw_brainvision.
I couldn't figure out how to set up the electrode location information in the rawData,since I don't have any additional localization file.
On another note,if I had nothing but the EEG data(with the std electrode locations) it is hard to use most of the inverse methods in mne-python, is that right?
Thanks!
-Lakshmi
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu> [mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] on behalf of Denis-Alexander Engemann [denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>]
Sent: Thursday, October 30, 2014 4:12 PM

To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Topomap with Brainvision EEG data

Hi Lakshmi,

Generally it would be better to use actual data, not randomly generated data to compare both routines.
Obviously the locations are different.
Do you happen to use any importing routine to get your data into MNE?
Which kind of data format do you use, natively?
The viz function you're using is quite low level and normally expects preprocessed channel locations.
We'll have a mini MNE sprint tomorrow in Paris on EEG, montages and io functionality.
We'll take a look at your case and get back to you.

Best,
Denis

2014-10-30 21:02 GMT+01:00 Lakshmi Krishnan <lakshmik at umd.edu<mailto:lakshmik at umd.edu>>:

Hi Denis,
Here is the link to sample sample scripts and figures for generating the topomap with a eeglab utility function and mne-python.

https://copy.com/djUllqUXi3lfSaiV

The matlab topoplot matches the figures provided by Brain vision in their documentation.I would be happy to use any other channel location file that's known to work with Brain Vision EEG data.
Thanks!
-Lakshmi
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu> [mne_analysis-bounces at nmr.mgh.harvard.edu<mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] on behalf of Denis-Alexander Engemann [denis.engemann at gmail.com<mailto:denis.engemann at gmail.com>]
Sent: Thursday, October 30, 2014 9:27 AM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] Topomap with Brainvision EEG data

Hi Lakshmi,

could you possibly share data snippets, an example script and maybe the different figures that you see?
Otherwise it will be difficult to understand what's wrong.

--Denis

2014-10-30 14:23 GMT+01:00 Lakshmi Krishnan <lakshmik at umd.edu<mailto:lakshmik at umd.edu>>:
Hello List,
I am trying to port all my Matlab analysis scripts into python and have trouble making a topomap with EEG data collected from a Brainvision system.
I am trying to use mne.viz.plot_topomap() with the channel location information that I know works with eeglab topoplot.
The resulting plot doesn't match the topomap I make with Matlab.
Any help to resolve this is much appreciated.
I am using mne version 0.9 from github.
Thanks!
-Lakshmi

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