[Mne_analysis] problem with reading raw data
Xiaoping Fang
xpfang4 at gmail.com
Mon Jun 17 18:09:15 EDT 2019
External Email - Use Caution
Hi Denis,
Thanks for helping! I uploaded two new files (one empty room recording and
one task) and both have the same issue. Here is the new link:
https://drive.google.com/drive/folders/1nAXAu9fitqv2Afc8nL2qScTRNbjttsTD?usp=sharing.
Please let me know if you cannot download them.
Are corrupted files fixable?
Thanks,
Xiaoping
On Mon, Jun 17, 2019 at 5:48 PM Denis A. Engemann <
denis-alexander.engemann at inria.fr> wrote:
> External Email - Use Caution
>
> Hi Xiaoping,
>
> I tried to read the file and reproduce your error.
> In my experience this type of error might be due to corrupted files.
> Can you try with another file or can you try copying over the same file
> once more from your server?
>
> Best,
> Denis
>
> > On Jun 17, 2019, at 5:14 PM, Xiaoping Fang <xpfang4 at gmail.com> wrote:
> >
> > External Email - Use Caution
> >
> >
> > Hello,
> >
> > I have trouble reading some of my raw data files. They seem pretty
> random -- two are empty room recordings from two different participants
> recorded at the end of the session, three are task files, while the other
> files are fine. The error is "file does not start with a file id tag".
> Below are the details. Could you help me with this? Thank you very much!
> >
> > Link to one of the data files:
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdrive.google.com%2Fopen%3Fid%3D1hwOH0Gh0KOqFpFl0-4HHlr6oZliROaL8&data=02%7C01%7Cxiaoping.fang%40pitt.edu%7C528e16b26694455a399908d6f36d90b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636964049247763303&sdata=J7r9XBqptA47pnKrANlIs6PcgGwIba%2BFTX7gFcQgupQ%3D&reserved=0
>
> >
> > Output:
> > Opening raw data file EmptyRoom_raw.fif...
> >
> >
> ---------------------------------------------------------------------------
> > ValueError
> > Traceback (most recent call last)
> >
> > <ipython-input-87-3e7740fb39a4> in <module>
> > 6 fname_projs = "erm-proj.fif"
> > 7 fname_erm_wproj = "EmptyRoom_wproj_raw.fif"
> > ----> 8 raw_erm = mne.io.read_raw_fif(fname_erm, preload=True)
> > 9 raw_erm.add_proj([],remove_existing=True)
> > 10 raw_erm.info['bads'] = ['MEG0432','MEG2233','MEG2543']
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/io/fiff/raw.py in
> read_raw_fif(fname, allow_maxshield, preload, verbose)
> > 468
> > """
> >
> > 469
> > return Raw(fname=fname, allow_maxshield=allow_maxshield,
> >
> > --> 470
> > preload=preload, verbose=verbose)
> >
> >
> >
> </Users/xif20/anaconda3/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-160>
> in __init__(self, fname, allow_maxshield, preload, verbose)
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/utils/_logging.py in
> wrapper(*args, **kwargs)
> > 87 with use_log_level(verbose_level):
> > 88 return function(*args, **kwargs)
> > ---> 89 return function(*args, **kwargs)
> > 90
> > return FunctionMaker.create(
> >
> > 91 function, 'return decfunc(%(signature)s)',
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/io/fiff/raw.py in
> __init__(self, fname, allow_maxshield, preload, verbose)
> > 83 raw, next_fname, buffer_size_sec = \
> > 84
> > self._read_raw_file(next_fname, allow_maxshield,
> >
> > ---> 85
> > preload, do_check_fname)
> >
> > 86 do_check_fname = False
> > 87 raws.append(raw)
> >
> >
> >
> >
> </Users/xif20/anaconda3/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-161>
> in _read_raw_file(self, fname, allow_maxshield, preload, do_check_fname,
> verbose)
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/utils/_logging.py in
> wrapper(*args, **kwargs)
> > 87 with use_log_level(verbose_level):
> > 88 return function(*args, **kwargs)
> > ---> 89 return function(*args, **kwargs)
> > 90
> > return FunctionMaker.create(
> >
> > 91 function, 'return decfunc(%(signature)s)',
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/io/fiff/raw.py in
> _read_raw_file(self, fname, allow_maxshield, preload, do_check_fname,
> verbose)
> > 151 whole_file = True
> > 152 fname_rep = _get_fname_rep(fname)
> > --> 153 ff, tree, _ = fiff_open(fname, preload=whole_file)
> > 154 with ff as fid:
> > 155 # Read the measurement info
> >
> >
> >
> >
> </Users/xif20/anaconda3/lib/python3.7/site-packages/mne/externals/decorator.py:decorator-gen-6>
> in fiff_open(fname, preload, verbose)
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/utils/_logging.py in
> wrapper(*args, **kwargs)
> > 87 with use_log_level(verbose_level):
> > 88 return function(*args, **kwargs)
> > ---> 89 return function(*args, **kwargs)
> > 90
> > return FunctionMaker.create(
> >
> > 91 function, 'return decfunc(%(signature)s)',
> >
> >
> >
> > ~/anaconda3/lib/python3.7/site-packages/mne/io/open.py in
> fiff_open(fname, preload, verbose)
> > 129 # Check that this looks like a fif file
> > 130 if tag.kind != FIFF.FIFF_FILE_ID:
> > --> 131 raise ValueError('file does not start with a file id
> tag')
> > 132
> >
> >
> > 133 if tag.type != FIFF.FIFFT_ID_STRUCT:
> >
> >
> >
> > ValueError: file does not start with a file id tag
> >
> >
> > Best,
> > Xiaoping
> >
> > --
> > Xiaoping Fang
> >
> > Graduate Student - Psychology
> > Learning Research and Development Center
> > Center for Neural Basis of Cognition
> > University of Pittsburgh
> >
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsites.google.com%2Fsite%2Fxpfang4&data=02%7C01%7Cxiaoping.fang%40pitt.edu%7C528e16b26694455a399908d6f36d90b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636964049247763303&sdata=svzRg72pCkGDSfZQSZaZDsa1bpM0RJ0PEwqgDEGpQvc%3D&reserved=0
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> >
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis&data=02%7C01%7Cxiaoping.fang%40pitt.edu%7C528e16b26694455a399908d6f36d90b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636964049247763303&sdata=yz9M3GPJXAZeXLhl9SLxmHqCZpxlVPPiGF7ar4KgL1A%3D&reserved=0
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
>
> https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Fmne_analysis&data=02%7C01%7Cxiaoping.fang%40pitt.edu%7C528e16b26694455a399908d6f36d90b9%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C636964049247763303&sdata=yz9M3GPJXAZeXLhl9SLxmHqCZpxlVPPiGF7ar4KgL1A%3D&reserved=0
>
--
Xiaoping Fang
Graduate Student - Psychology
Learning Research and Development Center
Center for Neural Basis of Cognition
University of Pittsburgh
https://sites.google.com/site/xpfang4
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20190617/6363668b/attachment-0001.html
More information about the Mne_analysis
mailing list