[Mne_analysis] Fwd: Problems with interpolation (newbie question)
Victor Ferat
victor.ferat at fcbg.ch
Tue Aug 27 11:31:52 EDT 2019
External Email - Use Caution
Hi Егор,
You may need to set the electrode positions with raw.set_montage<https://martinos.org/mne/dev/generated/mne.io.Raw.html#mne.io.Raw.set_montage>(montage=montage)
You can use montage = mne.channels.read_montage<https://martinos.org/mne/dev/generated/mne.channels.read_montage.html> to load built-in montage or create your own one using the class Montage<https://martinos.org/mne/dev/generated/mne.channels.Montage.html#mne.channels.Montage>
Victor
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Егор Сысоев <egor.sysoev2002 at gmail.com>
Sent: Tuesday, August 27, 2019 5:17 PM
To: mne_analysis at nmr.mgh.harvard.edu <mne_analysis at nmr.mgh.harvard.edu>
Subject: [Mne_analysis] Fwd: Problems with interpolation (newbie question)
External Email - Use Caution
Hi everybody,
Earlier I asked about a problem I was having with interpolation of EEG channels and one of the answers fixed my problem (.pick_types(eeg=True, exclude=())). However, there is apparently another problem with the same thing.
The error is:
ValueError: Could not extract channel positions for 72 channels
Here is a simplified version of the code, which still gives the same error:
import mne
data = '...\\NPh1.bdf' #path to file
raw = mne.io.read_raw_bdf(data, preload=True)
Info = raw.info<http://raw.info>
Info['bads'] = ['FC3']
raw.copy().pick_types(eeg=True, exclude=()).interpolate_bads()
The raw.info<http://raw.info> can be seen in the forwarded message below.
---------- Forwarded message ---------
От: Егор Сысоев <egor.sysoev2002 at gmail.com<mailto:egor.sysoev2002 at gmail.com>>
Date: чт, 22 авг. 2019 г. в 23:12
Subject: Problems with interpolation (newbie question)
To: <mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>>
Hi everybody,
I'm new to MNE analysis. I'm trying to interpolate bad channels in EEG (BioSemi) data, but there seems to be an error.
The raw.info<http://raw.info> looks like this:
<Info | 16 non-empty fields
bads : list | FC3
ch_names : list | Fp1, AF7, AF3, F1, F3, F5, F7, FT7, FC5, ...
chs : list | 73 items (EEG: 72, STIM: 1)
comps : list | 0 items
custom_ref_applied : bool | False
dev_head_t : Transform | 3 items
events : list | 0 items
highpass : float | 0.0 Hz
hpi_meas : list | 0 items
hpi_results : list | 0 items
lowpass : float | 104.0 Hz
meas_date : tuple | 2015-09-01 13:51:14 GMT
nchan : int | 73
proc_history : list | 0 items
projs : list | 0 items
sfreq : float | 512.0 Hz
acq_pars : NoneType
acq_stim : NoneType
ctf_head_t : NoneType
description : NoneType
dev_ctf_t : NoneType
dig : NoneType
experimenter : NoneType
file_id : NoneType
gantry_angle : NoneType
hpi_subsystem : NoneType
kit_system_id : NoneType
line_freq : NoneType
meas_id : NoneType
proj_id : NoneType
proj_name : NoneType
subject_info : NoneType
xplotter_layout : NoneType
>
And the error\warning when I write "raw.copy().pick_types(eeg=True).interpolate_bads()" is this:
<ipython-input-21-28f155242753>:1: RuntimeWarning: No bad channels to interpolate. Doing nothing...
raw.copy().pick_types(eeg=True).interpolate_bads()
As can be seen from the raw.info<http://raw.info>, there is one bad channel, and I can't figure out what the problem is.
Best regards,
Egor
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