[Mne_analysis] ctf file issues
Alexandre Gramfort
alexandre.gramfort at telecom-paristech.fr
Thu Jul 31 19:53:33 EDT 2014
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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