[Mne_analysis] ctf file issues

wgraves at psychology.rutgers.edu wgraves at psychology.rutgers.edu
Wed Jul 30 14:09:24 EDT 2014
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Hi Denis,

Thanks for the suggestions, and for being willing to take a look at a
snippet of data. Unfortunatley, when I run the first command you have as
written, this happens:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-55-ddfaa452efda> in <module>()
----> 1 raw.crop(None, 0.1)

/home/wgraves/data/ld_meg/scripts/src/mne/mne/fiff/base.pyc in crop(self,
tmin, tmax, copy)
    606             raise ValueError('tmin must be less than tmax')
    607         if tmin < 0.0:
--> 608             raise ValueError('tmin must be >= 0')
    609         elif tmax > max_time:
    610             raise ValueError('tmax must be less than or equal to
the max raw '

ValueError: tmin must be >= 0


So I tried this instead, which seems to work:
In [56]: raw.crop(1,1.1)
Out[56]: <Raw  |  n_channels x n_times : 303 x 61>

However, when I run:
raw.save('test-ctf_raw.fif')

it proceeds to save all 370 seconds of the file.

Anyway, I guess you must be right about the channel names, because when I
run:
In [54]: raw.ch_names

I get this:
Out[54]:
['UPPT001',
 'SCLK01-177',
 'BG1-3805',
 'BG2-3805',
 'BG3-3805',
 'BP1-3805',
 'BP2-3805',
 'BP3-3805',
 'BR1-3805',
 'BR2-3805',
 'BR3-3805',
 'G11-3805',
 'G12-3805',
 'G13-3805',
 'G22-3805',
 'G23-3805',
 'P11-3805',
 'P12-3805',
 'P13-3805',
 'P22-3805',
 'P23-3805',
 'Q11-3805',
 'Q12-3805',
 'Q13-3805',
 'Q22-3805',
 'Q23-3805',
 'R11-3805',
 'R12-3805',
 'R13-3805',
 'R22-3805',
 'R23-3805',
 'MLC11-3805',
 'MLC12-3805',
 'MLC13-3805',
 'MLC14-3805',
 'MLC15-3805',
 'MLC16-3805',
 'MLC17-3805',
 'MLC21-3805',
 'MLC22-3805',
 'MLC23-3805',
 'MLC24-3805',
 'MLC25-3805',
 'MLC31-3805',
 'MLC32-3805',
 'MLC41-3805',
 'MLC42-3805',
 'MLC51-3805',
 'MLC52-3805',
 'MLC53-3805',
 'MLC54-3805',
 'MLC55-3805',
 'MLC61-3805',
 'MLC62-3805',
 'MLC63-3805',
 'MLF11-3805',
 'MLF12-3805',
 'MLF13-3805',
 'MLF14-3805',
 'MLF21-3805',
 'MLF22-3805',
 'MLF23-3805',
 'MLF24-3805',
 'MLF25-3805',
 'MLF31-3805',
 'MLF32-3805',
 'MLF33-3805',
 'MLF34-3805',
 'MLF35-3805',
 'MLF41-3805',
 'MLF42-3805',
 'MLF43-3805',
 'MLF44-3805',
 'MLF45-3805',

and so on... with nothing that looks like those nice, sensible channel
names you listed.

I suppose I somehow need to pair the CTF channle selections file with this
dataset, but outside of the interactive mne_browse_raw interace, I don't
know how to do that.

Thanks,
Will


> Hi will,
>
> could you share a small snippet (e.g. 100 ms) of your data like that:
>
> raw.crop(None, 0.1)
> raw.save('my-ctf-raw.fif')
>
> I suspect there is some channel type in your data whic is not classified
> as
> one of these:
>
> ['eeg', 'eog', 'ecg', 'emg', 'ref_meg', 'stim', 'resp', 'misc', 'chpi',
> 'syst', 'ias', 'exci']
>
> Maybe your reference channels are not marked as such.
> You could try to identify them by name and remove them just for the
> purpose
> of plotting using
>
> `raw.drop_channels(channel_names)`
>
> Best,
> Denis
>
> On Wed, Jul 30, 2014 at 6:00 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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