[Mne_analysis] concatenation raws and events

J.A. Entakli jae40 at cam.ac.uk
Thu Sep 11 11:42:15 EDT 2014
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Hi,

I would like, for all the MEG processing, to work only on one big raw 
file (that's to say bloc 1 + bloc 2). Concerning the events, I extracted 
the events (events.txt) from mne_browse and I modified manually some 
values in these files (with Matlab).

So actually, I have 2 blocs with 1 events.txt file each corresponding.
raw_fname1= '...' with event_fname1= '...'
raw_fname2= '...' with event_fname2= '...'

Cheers,
John


On 11/09/2014 16:19, dgw wrote:
> Hi John,
> 
> Can you explain in more detail what you are trying to do? The original
> events are in the raw fif files. Do you want to change them or are you
> worried you changed them, or have you already changed them?
> 
> (if you already have changed them, where did you change them: in the
> raw file? how did you change them? etc.)
> 
> HTH,
> D
> 
> On Thu, Sep 11, 2014 at 11:14 AM, J.A. Entakli <jae40 at cam.ac.uk> wrote:
>> Hi D,
>> I understand but the problem is that I modified manually some number 
>> in
>> the events file and now I not able to extract directly them. Tell me 
>> if
>> I make a mistake. I am a really beginner.
>> 
>> Thanks,
>> John
>> 
>> On 11/09/2014 16:07, dgw wrote:
>>> You should be able to read the events straight from the raw object.
>>> (mne.find_events). This is the safest way to deal with events.
>>> 
>>> HTH
>>> D
>>> 
>>> On Thu, Sep 11, 2014 at 11:06 AM, J.A. Entakli <jae40 at cam.ac.uk> 
>>> wrote:
>>>> Thank you Steve,
>>>> 
>>>> I suppose something like that:
>>>> raws = mne.io.Raw(['raw1_fname','raw2_fname'])
>>>> 
>>>> and what about the events??
>>>> 
>>>> Bests,
>>>> Jonathan
>>>> 
>>>> On 11/09/2014 15:58, Stephen Politzer-Ahles wrote:
>>>>> Hi Jonathan,
>>>>> 
>>>>> When you read your raw file, you can pass the function a list of
>>>>> filenames (instead of one filename) to automatically read all those
>>>>> files into a single Raw object. Then you shouldn't need to worry
>>>>> about
>>>>> concatenating later.
>>>>> 
>>>>> Best,
>>>>> Steve
>>>>> 
>>>>> Stephen Politzer-Ahles
>>>>> New York University, Abu Dhabi
>>>>> Neuroscience of Language Lab
>>>>> http://www.nyu.edu/projects/politzer-ahles/ [5]
>>>>> 
>>>>> On Thu, Sep 11, 2014 at 6:44 PM, J.A. Entakli <jae40 at cam.ac.uk>
>>>>> wrote:
>>>>> 
>>>>>> Hello Everybody,
>>>>>> During my experiment I recorded 2 blocs per subject. I am just
>>>>>> started
>>>>>> with mne_python.
>>>>>> 
>>>>>> I have two questions in one ::
>>>>>> 1) I would like to know how can I concatenate the blocs and above
>>>>>> all
>>>>>> the events (corresponding to each bloc) to have just one bloc.
>>>>>> In brief, for each subject I have one bloc with its events and
>>>>>> another
>>>>>> bloc with its events also.
>>>>>> 
>>>>>> raw_fname1= '...'
>>>>>> raw_fname2= '...'
>>>>>> event_fname1= '...'
>>>>>> event_fname2= '...'
>>>>>> 
>>>>>> raw1 = io.Raw(raw_fname1)
>>>>>> raw2 = io.Raw(raw_fname2)
>>>>>> 
>>>>>> events1 = mne.read_events(event_fname1)
>>>>>> events2 = mne.read_events(event_fname2)
>>>>>> events_list = [events1,events2]
>>>>>> 
>>>>>> raw_conc= concatenate_raws([raw1,raw2], events_list=events_list)
>>>>>> 
>>>>>> Until here I think these several code lines work correctly...
>>>>>> 
>>>>>> 2) But when I try to extract the epochs from raw_conc I have some
>>>>>> error
>>>>>> messages (concerning I think the events_list)
>>>>>> 
>>>>>> picks =
>>>>>> mne.pick_types(raw1.info
>>>>>> [1],meg='mag',eeg=False,ecg=False,eog=False,stim=False,
>>>>>> exclude='bads')
>>>>>> epochs = mne.Epochs(raw, events_list, event_id, tmin, tmax,
>>>>>> picks=picks,
>>>>>> baseline= baseline, reject=reject)
>>>>>> 
>>>>>> The aim of both questions is to use the tfr_morlet function which
>>>>>> asks
>>>>>> in input the epochs.
>>>>>> 
>>>>>> power, itc = tfr_morlet(epochs, freqs=freqs, n_cycles=n_cycles,
>>>>>> use_fft=False, return_itc=True, decim=3,n_jobs=1)
>>>>>> 
>>>>>> Someone has an idea about this?
>>>>>> 
>>>>>> Bests,
>>>>>> 
>>>>>> Jonathan
>>>>>> --
>>>>>> Dr Jonathan Entakli - Research Associate Post doctoral position
>>>>>> 
>>>>>> Department of Psychology
>>>>>> University of Cambridge, Downing St
>>>>>> Cambridge CB2 3EB
>>>>>> 
>>>>>> Sir William Hardy Building
>>>>>> Office : 314
>>>>>> Mobile : 07778 692 458
>>>>>> 
>>>>>> http://www.viscog.psychol.cam.ac.uk/ [2]
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>>>>> 
>>>>> 
>>>>> 
>>>>> Links:
>>>>> ------
>>>>> [1] http://raw1.info
>>>>> [2] http://www.viscog.psychol.cam.ac.uk/
>>>>> [3] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>> [4] http://www.partners.org/complianceline
>>>>> [5] http://www.nyu.edu/projects/politzer-ahles/
>>>>> 
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>>>> 
>>>> --
>>>> Dr Jonathan Entakli - Research Associate
>>>> 
>>>> Department of Psychology
>>>> University of Cambridge, Downing St
>>>> Cambridge CB2 3EB
>>>> 
>>>> Sir William Hardy Building
>>>> Office : 314
>>>> Mobile : 07778 692 458
>>>> 
>>>> http://www.viscog.psychol.cam.ac.uk/
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>>>> Mne_analysis mailing list
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>> 
>> --
>> Dr Jonathan Entakli - Research Associate
>> 
>> Department of Psychology
>> University of Cambridge, Downing St
>> Cambridge CB2 3EB
>> 
>> Sir William Hardy Building
>> Office : 314
>> Mobile : 07778 692 458
>> 
>> http://www.viscog.psychol.cam.ac.uk/
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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-- 
Dr Jonathan Entakli - Research Associate

Department of Psychology
University of Cambridge, Downing St
Cambridge CB2 3EB

Sir William Hardy Building
Office : 314
Mobile : 07778 692 458

http://www.viscog.psychol.cam.ac.uk/

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