[Mne_analysis] how to save source estamates from epoched data set with multiple events

[David I Leitman]

thanks I have been using this example as a base but I was curious about the following:
1. can stc.extract_label_time_course  work on a epoched data . fif file containing all my event condtions
2.  lets say I want to extract  as a time course just the vertices with the center of mass or perhaps an roi reflecting this vertices and a small number of neighboring vertices instead of the mean of a whole anatomic roi label. how could I do that?
3 ) with np.save can I also ad a vector that corresponds to the event type that each epoch represents?

thanks //dave
On Jan 13, 2014, at 5:43 PM, Alexandre Gramfort wrote:

> hi David,
> 
> have a look at:
> 
> http://martinos.org/mne/stable/auto_examples/inverse/plot_label_source_activations.html
> 
> extract_label_time_course will give you a time series per stc, then you can make
> an array from all time courses and save it as a numpy binary file with np.save
> 
> let me know if you need more help
> 
> HTH
> Alex
> 
> 
> On Mon, Jan 13, 2014 at 7:58 PM, David Leitman
> <leitman at mail.med.upenn.edu> wrote:
>> Hi all,
>> I am trying to extract from a structural roi a time series source estimate for each one of the epoch in each of my conditions
>> 
>> first I read in the saved epoched data fif file:
>> 
>> epochs=mne.read_epochs(fname_epoched)
>> 
>> next I apply the inverse operator that I created using the evoked data and the anatomic label previously created  and execute the following:
>> 
>> stcs = apply_inverse_epochs(epochs,inverse_operator, lambda2, method, anat_label1,
>>                            pick_ori="normal")
>> 
>> what I would like to do next is calculate the mean activation within this roi comprising 480 vertices. so that I have one average value for each of my epochs and conditions and save an output matrix comprising time series for each epoch and including a vector for event id
>> 
>> I tried picking up from the a similar stage in the plot_compute_mne_inverse_epochs_in_label.py substituting my commands above for
>> 
>> # Read epochs
>> epochs = mne.Epochs(raw, events, event_id, tmin, tmax, picks=picks,
>>                    baseline=(None, 0), reject=dict(mag=4e-12, grad=4000e-13,
>>                                                    eog=150e-6))
>> 
>> # Compute inverse solution and stcs for each epoch
>> stcs = apply_inverse_epochs(epochs, inverse_operator, lambda2, method, label,
>>                            pick_ori="normal")
>> 
>> mean_stc = sum(stcs) / len(stcs)
>> 
>> 
>> but mean_stc is not what I want and stcs does not have attribute save like for example stc.save
>> 
>> any help would be appreciated
>> thanks dave
>> 
>> 
>> 
>> 
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David I. Leitman PhD

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