[Mne_analysis] ctf file issues
William Graves
wgraves at psychology.rutgers.edu
Thu Jul 31 20:52:05 EDT 2014
Very nice, Alex. Thank you!
-Will
---
William W. Graves, Ph.D.
Assistant Professor, Department of Psychology
Rutgers, The State University of New Jersey
Smith Hall, Room 337
101 Warren Street, Newark, NJ 07102
Voice: 973-353-3947
Fax: 973-353-1171
http://lbbil.rutgers.edu
On Jul 31, 2014, at 7:53 PM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> wrote:
> hi Will,
>
> I just fixed the pb on current master. The fix will be included in
> v0.8.1 in a few days.
>
> https://github.com/mne-tools/mne-python/commit/597681d9a7f9516bc8275053001b070f02f287a2
>
> Alex
>
> On Wed, Jul 30, 2014 at 8:37 PM, Denis-Alexander Engemann
> <denis.engemann at gmail.com> wrote:
>> Hi Will,
>>
>> I meanwhile opened an issue on github. People interested in the solution can
>> follow the development there.
>>
>> Best,
>> Denis
>>
>>
>>
>> On Wed, Jul 30, 2014 at 8:17 PM, Denis-Alexander Engemann
>> <denis.engemann at gmail.com> wrote:
>>>
>>> Hi Will,
>>>
>>> sorry for the confusion.
>>>
>>> This line would work (crop makes a copy by default and `None` is only
>>> valid for Epochs and Evokeds):
>>>
>>> raw.crop(0, 0.1, copy=False)
>>> raw.save('my-ctf-raw.fif')
>>>
>>> # should fit into an email as attachment
>>>
>>> Since I don't know the CTF system very well the channels don't help as
>>> such. It's more relevant what's in the raw.info dict, actually the type
>>> information used inside the plotting routine is not inferred from the
>>> channels names.
>>>
>>> Denis
>>>
>>>
>>>
>>> On Wed, Jul 30, 2014 at 8:09 PM, <wgraves at psychology.rutgers.edu> wrote:
>>>>
>>>> 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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