[Mne_analysis] ctf file issues

[wgraves at psychology.rutgers.edu]

Thanks Matti. You're right, of course. When I invoke mne_browse_raw this way:

mne_browse_raw --digtrig UPPT001 --sel
$MNE_ROOT/share/mne/mne_browse_raw/mne_browse_raw_CTF_275.sel

I can open the raw file and view the traces. It also looks like the entire
6-min run is continuous, even though it was acquired in short event-keyed
epochs, so no need for an additional concatenation step I guess.

Thanks again!

-Will

>
> 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
>
>
>
>
>
>
>
>
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