[Mne_analysis] error when initiating a raw object
Dykstra, Andrew
Andrew.Dykstra at med.uni-heidelberg.de
Wed Jan 9 08:22:57 EST 2013
Hi Alex,
Yes, I can open the file with mne_browse_raw and can create evoked
responses from it via mne_process_raw which themselves can be read via
mne.fiff.read_evoked.
An additional piece of information I just discovered: I can open the
raw file straight from the acquisition. The file that I can cannot open
was written via a modified version of fiff_write_raw_segment.m (buffer
adjusted from 30 to 0.5 seconds) after some preprocessing in MATLAB. I
haven't run into this issue with other subjects processed using the
exact same stream. There are links to three files below. The first two
are from the troublesome subject. The last is a raw file, after MATLAB
preprocessing, that can be opened with mne.fiff.Raw.
http://ubuntuone.com/69KPvr8lU4Goz7Hkm7MPJH
http://ubuntuone.com/3QiiHgl7Oxr5astCIFwv6K
http://ubuntuone.com/2kcJZjdCZJg2xpdAymGcI3
Thanks for the help,
Andy
p.s. happy to learn that ICA has now been incorporated into the python
package. This closes my data analysis loop to keep me in shell/python.
Thanks Alex/Denis.
--
Andrew R. Dykstra, PhD
Auditory Cognition Lab
Neurologie und Poliklinik
Universitätsklinikum Heidelberg
Im Neuenheimer Feld 400
69120 Heidelberg
"How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
On 01/08/2013 07:09 PM, Alexandre Gramfort wrote:
> hi Andy,
>
> can you read this file otherwise with mne_browse_raw or mne_process_raw?
>
> if yes can you share the file via dropbox or any other service?
>
> thanks
> Alex
>
> On Tue, Jan 8, 2013 at 6:14 PM, Dykstra, Andrew
> <Andrew.Dykstra at med.uni-heidelberg.de> wrote:
>> Dear MNE community,
>>
>> I am experiencing an error that I don't understand when trying to create
>> a raw object in Python. The traceback is below, and I only get this
>> with the raw files from one subject. I initially thought that it could
>> be due to the abnormally large file sizes of this subject's raw data
>> (~700 Mb), but I have one other subject whose raw data were comparable
>> and I can create raw objects from those data without issue.
>>
>> Has anyone experienced this?
>>
>> Cheers,
>> Andy
>>
>> error Traceback (most recent call last)
>> /home/andrew/Experiments/Awareness_wo_Attention/<ipython-input-8-5fbcd28d6772>
>> in <module>()
>> ----> 1
>> runfile(r'/home/andrew/Experiments/Awareness_wo_Attention/py_tmp_check_dataset_channels.py',
>> wdir=r'/home/andrew/Experiments/Awareness_wo_Attention')
>>
>> /usr/local/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.pyc
>> in runfile(filename, args, wdir, namespace)
>> 485 pass
>> 486 os.chdir(wdir)
>> --> 487 execfile(filename, namespace)
>> 488 sys.argv = ['']
>> 489 namespace.pop('__file__')
>>
>> /home/andrew/Experiments/Awareness_wo_Attention/py_tmp_check_dataset_channels.py
>> in <module>()
>> 48 for block in range(2):
>> 49 fname.append(data_path + '/' + subject + '/meg/' +
>> subject + '_block' + str(block+1) + '_cleaned_raw.fif')
>> ---> 50 raw.append(mne.fiff.Raw(fname[block]))
>> 51 chan.append(raw[block].ch_names)
>> 52 chan.append([x for x in chan[0] if x not in set(chan[1])])
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>> in dec(*args, **kwargs)
>> 263 return ret
>> 264 else:
>> --> 265 return function(*args, **kwargs)
>> 266
>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>> source
>>
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/raw.pyc
>> in __init__(self, fnames, allow_maxshield, preload, verbose, proj_active)
>> 83
>> 84 raws = [self._read_raw_file(fname, allow_maxshield,
>> preload)
>> ---> 85 for fname in fnames]
>> 86
>> 87 _check_raw_compatibility(raws)
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>> in dec(*args, **kwargs)
>> 263 return ret
>> 264 else:
>> --> 265 return function(*args, **kwargs)
>> 266
>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>> source
>>
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/raw.pyc
>> in _read_raw_file(self, fname, allow_maxshield, preload, verbose)
>> 137 ext = os.path.splitext(fname)[1].lower()
>> 138 whole_file = preload if '.gz' in ext else False
>> --> 139 fid, tree, _ = fiff_open(fname, preload=whole_file)
>> 140
>> 141 # Read the measurement info
>>
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/utils.pyc
>> in dec(*args, **kwargs)
>> 263 return ret
>> 264 else:
>> --> 265 return function(*args, **kwargs)
>> 266
>> 267 # set __wrapped__ attribute so ?? in IPython gets the right
>> source
>>
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/open.pyc
>> in fiff_open(fname, preload, verbose)
>> 83 while tag.next >= 0:
>> 84 pos = fid.tell()
>> ---> 85 tag = read_tag_info(fid)
>> 86 tag.pos = pos
>> 87 directory.append(tag)
>>
>> /usr/local/lib/python2.7/dist-packages/mne-0.6.git-py2.7.egg/mne/fiff/tag.pyc
>> in read_tag_info(fid)
>> 67 """
>> 68 s = fid.read(4 * 4)
>> ---> 69 tag = Tag(*struct.unpack(">iiii", s))
>> 70 if tag.next == 0:
>> 71 fid.seek(tag.size, 1)
>>
>> error: unpack requires a string argument of length 16
>>
>> --
>> Andrew R. Dykstra, PhD
>> Auditory Cognition Lab
>> Neurologie und Poliklinik
>> Universitätsklinikum Heidelberg
>> Im Neuenheimer Feld 400
>> 69120 Heidelberg
>>
>> "How small the cosmos. How paltry and puny compared to human consciousness . . . to a single individual recollection." - Vladimir Nabokov
>>
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