[Mne_analysis] Problem exporting data from Matlab (Fieldtrip/SPM) for mne-python

Alexandre Gramfort alexandre.gramfort at telecom-paristech.fr
Mon Dec 16 08:18:35 EST 2013
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hi nick,

well I guess you should report the problem on the fieldtrip mailing list,
as it's on a bug on their side if the fif file written is not
recognized as a raw file.

did you try to load the same files with the MNE C commands? with neuromag tools?

out of curiosity what processing are you doing with SPM?

Best,
Alex



On Mon, Dec 16, 2013 at 2:11 PM, Nick Ward <ward.nickjames at gmail.com> wrote:
> Hi.
>
> I'm having trouble getting set of MEG data to load in Python (both 2 and 3).
> I'm exporting the data from SPM by converting to Fieldtrip raw format
> (spm2fieldtrip), and then calling fieldtrip2fiff.
> I get a few warnings here, but the file is saved nonetheless:
>
>> the input is raw data with 340 channels and 120 trials
>> Warning: the data does not contain a trial definition
>>   In utilities/private/warning_once at 158
>>   In utilities/private/fixsampleinfo at 66
>>   In ft_datatype_raw at 154
>>  In ft_checkdata at 224
>>   In fieldtrip2fiff at 57
>>   In export at 8
>> Warning: reconstructing sampleinfo by assuming that the trials are
>> consecutive > segments of a continuous recording
>>  In utilities/private/warning_once at 158
>>  In utilities/private/fixsampleinfo at 79
>>  In ft_datatype_raw at 154
>>  In ft_checkdata at 224
>>  In fieldtrip2fiff at 57
>>  In export at 8
>> Reconstructing channel locations, it might be inaccurate
>> Unknown channel type refmag, assigned to meggrad....
>
> In Python I then try and load the data with mne.fiff.Raw('data.fif'), but
> get an exception:
>
>> /usr/lib/python2.7/site-packages/mne/fiff/raw.pyc in _read_raw_file(self,
>> fname, allow_maxshield, preload, compensation, verbose)
>>     191             else:
>>     192                 if len(raw_node) == 0:
>> --> 193                     raise ValueError('No raw data in %s' % fname)
>>     194
>>     195         if len(raw_node) == 1:
>> ValueError: No raw data in data.fif
>
> I've inspected what is loaded in the debugger, and it appears as if the file
> is being read. An exception is thrown however when there are no nodes found
> in the meas structure containing FIFFB_RAW_DATA or FIFFB_CONTINUOUS_DATA.
>
> I'm not familiar with the FIFF file format, so am wondering if anyone knows
> whether it is likely the failure to load the data is due to the warnings
> given at the Matlab end, or I should be looking elsewhere?
>
> Cheers,
> Nick
>
>
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