[Mne_analysis] BrainVision files

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Tue Jan 5 16:10:14 EST 2016
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Jona and Teon. Any thought on this?

thanks
Alex

On Tue, Jan 5, 2016 at 5:56 PM, Boris BURLE <boris.burle at univ-amu.fr> wrote:

> Hi again,
>
> Trying to find the issue, I realized that my installed version of mne
> was pretty old (0.8.6), and that this issue has already been fixed (at
> least it is in the dev version...). I apologize for that...
>
> But I found another issue:
>
> If I read correctly, it looks like line 201 of _read_vmrk_events assumes
> that response triggers name must contain an integer, probably
> considering that the names are "Rxxx", with "xxx" being integers.
> However, this is not a requirement of the file format and, especially
> after some preprocessing, the triggers names may have been changed to
> pure text (for example 'LeftResp'). In this case, the code does not seem
> to work, since 'trigger' is None, and line 206 issues an error:
>
>      trigger += response_trig_shift
> TypeError: unsupported operand type(s) for +=: 'NoneType' and 'int'
>
> Am I reading the code correctly?
>
>         Thanks in advance,
>                 B.
>
>
>
>
>
> On 05/01/2016 13:32, Alexandre Gramfort wrote:
> > hi Boris,
> >
> > our test data are in:
> >
> >
> https://github.com/mne-tools/mne-python/tree/master/mne/io/brainvision/tests/data
> >
> > don't hesitate to share a file so we can patch the reader to fix the
> issue.
> >
> > Best,
> > Alex
> >
> > On Tue, Jan 5, 2016 at 10:17 AM, Boris BURLE <boris.burle at univ-amu.fr>
> wrote:
> >> Dear colleagues,
> >>
> >> I'm just starting to use MNE-python, and I face a problem opening
> >> BrainVisionAnalyer files. When calling the
> >> "mne.io.read_raw_brainvision", I get the following error (full traceback
> >> at the end):
> >>
> >> --> 462     params, settings = settings.split('[Comment]')
> >>       463     cfg = configparser.ConfigParser()
> >>       464     if hasattr(cfg, 'read_file'):  # newer API
> >>
> >> ValueError: need more than 1 value to unpack
> >>
> >> It appears that 'read_raw_brainvision' is searching for a "section"
> >> untitled "Comment" in the header (vhdr) file. I have been using
> >> BrainVision files quite a lot (actually, I would like to get rid of it
> >> by using mne-python...), and I never encountered such a "Comment" field
> >> in my vhdr files. However, I always worked with data **exported** from
> >> BrainVision, not acquired with it. So I guess the "Comment" field the
> >> parser is searching might come from the files created by
> >> BrainVisionRecorder. But since I do not have any such file, I cannot
> check.
> >>
> >> I do have python code that, I believe, open all variants of files
> >> **exported** from BrainVisionAnalyser (be they ASCII or binary, 16, 32
> >> ... bits etc...). The code outputs a dictionary for the header (vhdr)
> >> file, a numpy.array for the data, and a list of events for the
> >> markers/events/triggers. Although I guess it should also open files
> >> created by BrainVisionRecorder, I cannot be sure.
> >>
> >> So, if someone could provide me with a small file that is currently
> >> openable by "mne.io.read_raw_brainvision", I would be happy to check
> >> whether my code also open it. And, if you find it useful, I would be
> >> more than happy to share the code and adapt it to mne-python (with a bit
> >> of help from you, probably ...)
> >>
> >>     All the best,
> >>       B.
> >>
> >> full traceback:
> >> In [4]: mne.io.read_raw_brainvision('COUBA_EMG_PC_CompLeft.vhdr')
> >> Extracting eeg Parameters from COUBA_EMG_PC_CompLeft.vhdr...
> >>
> ---------------------------------------------------------------------------
> >> ValueError                                Traceback (most recent call
> last)
> >> <ipython-input-4-b9123e703050> in <module>()
> >> ----> 1 mne.io.read_raw_brainvision('COUBA_EMG_PC_CompLeft.vhdr')
> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc in
> >> read_raw_brainvision(vhdr_fname, elp_fname, elp_names, preload,
> >> reference, eog, ch_names, verbose)
> >>       681     """
> >>       682     raw = RawBrainVision(vhdr_fname, elp_fname, elp_names,
> preload,
> >> --> 683                          reference, eog, ch_names, verbose)
> >>       684     return raw
> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc in
> >> __init__(self, vhdr_fname, elp_fname, elp_names, preload, reference,
> >> eog, ch_names, verbose)
> >>
> >> /usr/lib/python2.7/dist-packages/mne/utils.pyc in verbose(function,
> >> *args, **kwargs)
> >>       549         return ret
> >>       550     else:
> >> --> 551         ret = function(*args, **kwargs)
> >>       552         return ret
> >>       553
> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc in
> >> __init__(self, vhdr_fname, elp_fname, elp_names, preload, reference,
> >> eog, ch_names, verbose)
> >>        82         self.info, self._eeg_info, events =
> >> _get_eeg_info(vhdr_fname,
> >>        83
> >> elp_fname, elp_names,
> >> ---> 84
> >> reference, eog)
> >>        85         self.set_brainvision_events(events)
> >>        86         logger.info('Creating Raw.info structure...')
> >>
> >> /usr/lib/python2.7/dist-packages/mne/io/brainvision/brainvision.pyc in
> >> _get_eeg_info(vhdr_fname, elp_fname, elp_names, reference, eog)
> >>       460         settings = f.read()
> >>       461
> >> --> 462     params, settings = settings.split('[Comment]')
> >>       463     cfg = configparser.ConfigParser()
> >>       464     if hasattr(cfg, 'read_file'):  # newer API
> >>
> >> ValueError: need more than 1 value to unpack
> >>
> >> In [5]:
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