[Mne_analysis] need help to plot EEG topomaps with mne
jeanremi.king at gmail.com
Mon Jun 20 04:13:43 EDT 2016
to complete Jaakko's answer, you can plot 3D EEG projection using mne.viz
import.evoked_field. For example:
import os.path as op
from mne.forward import make_field_map
from mne.viz import plot_evoked_field
# get data
data_path = mne.datasets.sample.data_path()
subjects_dir = data_path + '/subjects'
trans_fname = op.join(data_path, 'MEG', 'sample',
fname = op.join(data_path, 'MEG', 'sample', 'sample_audvis-ave.fif')
evoked = mne.read_evokeds(fname, baseline=(None, 0), proj=True)
# select eeg channels only
# plot field maps
maps = make_field_map(evoked, trans=trans_fname, subjects_dir=subjects_dir,
subject='sample', n_jobs=-1, meg_surf='head')
plot_evoked_field(evoked, maps, time=.1)
Hope that helps,
On 20 June 2016 at 09:00, Jaakko Leppäkangas <jaeilepp at student.jyu.fi>
> Hi Mathieu,
> currently there is no way to project to 3d.
> For the second point you could use a montage when reading the data. The
> readers for EEG data have a montage parameter that you could use to set the
> channel locations (see for example
> In your case, since you have some custom locations, one option would be to
> manually add entries for 'OL' and 'OR' to the standard_1020.elc file, if
> you know their locations.
> On 18 June 2016 at 20:56, Servant Mathieu <servant.mathieu at gmail.com>
>> I'm new to mne, and would like to compute some topographic voltage maps
>> from my EEG grand-averaged data.
>> I have two specific questions:
>> (i) The plot_topomap function plots 2D maps. Is there a way to plot 3D
>> (ii) My data_ is a 19 (electrodes) x 300 (datapoints) numpy array.
>> Sampling rate was 250 Hz, and the 300 datapoints correspond to a -200 1000
>> ms epoch (0 being the stimulus-locking event).
>> -Is there a simple way to plot topographies at say, 300 ms after stimulus
>> onset, or topographies over the average of a given time window (300-500ms
>> after stimulus onset)?
>> -I need to provide the (x,y) coordinates for each EEG channel. My
>> channels are:
>> electrodes =
>> These electrodes are standard international 10/20 System sites, except OL
>> (halfway between 01 and T5) and OL (halfway between 02 and T6). Given these
>> locations, which coordinate array should I provide to the plot_topomap
>> function ?
>> Thanks for your help!
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> HelpLine at
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