[Mne_analysis] ctf file issues

[Matti Hamalainen]

Hi Will,

In mne_browse_raw you need to create channel selections suitable for the CTF data to display them. There is a file  $MNE_ROOT/share/mne/mne_browse_raw/mne_browse_raw_CTF_275.sel which contains selections for the 275-channel CTF system.

- Matti

On Jul 30, 2014, at 12:00 PM, wgraves at psychology.rutgers.edu wrote:

> Hello MNE Experts,
> 
> In trying to deal with CTF files for the first, time I'm running into some
> issues that I don't understand and hope someone can easily help with. I
> used the mne_ctf2fiff command to convert to fiff, but I can't visualize
> the resulting file in mne_browse_raw (it loads without error but just
> looks blank). Similarly, all the steps for loading a segment of the file
> as raw data in mne_python work without error, until I do "raw.plot()",
> when I get this error:
> 
> In [20]: raw.plot()
> ---------------------------------------------------------------------------
> RuntimeError                              Traceback (most recent call last)
> <ipython-input-20-d4ffb847f525> in <module>()
> ----> 1 raw.plot()
> 
> /home/wgraves/data/ld_meg/scripts/src/mne/mne/fiff/base.pyc in plot(raw,
> events, duration, start, n_channels, bgcolor, color, bad_color,
> event_color, scalings, remove_dc, order, show_options, title, show, block)
>    846         return plot_raw(raw, events, duration, start, n_channels,
> bgcolor,
>    847                         color, bad_color, event_color, scalings,
> remove_dc,
> --> 848                         order, show_options, title, show, block)
>    849
>    850     @verbose
> 
> /home/wgraves/data/ld_meg/scripts/src/mne/mne/viz.pyc in plot_raw(raw,
> events, duration, start, n_channels, bgcolor, color, bad_color,
> event_color, scalings, remove_dc, order, show_options, title, show, block)
>   2778     inds = np.concatenate(inds).astype(int)
>   2779     if not len(inds) == len(info['ch_names']):
> -> 2780         raise RuntimeError('Some channels not classified, please
> report '
>   2781                            'this problem')
>   2782
> 
> RuntimeError: Some channels not classified, please report this problem
> 
> Unfortunately, the data were collected in short epochs keyed to the events
> rather than continuously. My original plan was to use
> mne.fiff.concatenate_raws to concatenate across epochs/events, but I
> couldn't figure out how to make that work either (perhaps because I don't
> know what the "raw" argument is supposed to look like, and I can't find an
> example).
> 
> Anyway, I would gratly appreciate any help or insight anyone can share.
> 
> Thanks,
> Will
> 
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> 
> 



---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org