[Mne_analysis] running ICA on eeg data - kernel failing

[Sammi Chekroud]

This is fixed: seemed to be a problem with numpy/scipy. Updating them to
newer versions solved this problem!
ᐧ

On 11 April 2017 at 08:54, Sammi Chekroud <sammi.r.chekroud at gmail.com>
wrote:

> Hi all,
>
> I'm new to mne so sorry if this is a noob question, but for some reason
> both ICA and interpolate_bads seem to keep breaking down my python kernel
> when i try to run them. Any suggestions? more details below (including code
> used)
>
> - running version 0.14dev0 to read the cnt format as that didn't work on
> the stable version initially
> - reading EEG data from the CNT format:
>
> *data = mne.io.read_raw_cnt(fname, montage = 'standard_1005', date_format
> = 'dd/mm/yy', eog = ['VEOG', 'HEOG'], misc = ['RM'], preload = True)*
>
> - rereferencing (to 'RM' channel) and resampling to 250hz, then filtering
> between 0.1 and 40Hz
>
> *# I know this is creating new vars, but this is deliberate*
>
> *reref = data.set_eeg_reference(ref_channels = ['RM'])*
>
> *resamp = reref.resample(250)*
> *filtered = resamp.filter(0.1,40)*
>
> it will extract events and epoch data properly, e.g.
>
> *encodingEpochs = mne.Epochs(filtered, events, events_encode, tmin, tmax,
> baseline = baseline, preload = True)*
>
> if I try to ICA on either the filtered data:
>
> *ica = mne.preprocessing.ICA(n_components=0.95).fit(filtered)*
>
> or on the epoched data:
>
> *ica = mne.preprocessing.ICA(n_components=0.95).fit(encodingEpochs)*
>
> then I get the following:
>
> Fitting ICA to data using 61 channels
> Please be patient, this may take some time
> Inferring max_pca_components from picks
>
>
>
> *It seems the kernel died unexpectedly. Use 'Restart Kernel' to continue
> using this console*
> this also happens if I try to interpolate bad channels, e.g.:
>
>
>
>
> *filtered.interpolate_bads(reset_bads=False)*
> Sorry for the potentially excessive info, but hope it clarifies the
> problem that I'm having! Any help would be greatly appreciated.
>
> Thanks!
>
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