[Mne_analysis] Fwd: Plotting power spectra of estimates on mne_analyze

Andres Felipe Salazar Gomez asalazar at nmr.mgh.harvard.edu
Thu Aug 27 00:30:12 EDT 2009
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Thank you very much everybody for your comments and collaboration.
I was able to create the files.

Now, I have another question:  How can I make visible the stc files in
mne_analyze?

After loading a surface in mne_analyze I load the stc file in Managing
overlays. After selecting the file I do not see any data on the surface or
any way to set a threshold to see my results.

What should I do in order to visualize the data?

Thanks very much for any comments on this regard,

-- Andrés


> Hi Andres,
>
> if you are talking about the hemisphere of the vertices. This will
> depend on your matlab scripts. You should specify and specifically
> choose each hemisphere. I don't have the manual in front of me, but I
> am sure there is a description of the forward matrix structure in it.
> This will tell you exactly how to do what you want. I believe the
> matlab section is chapter 10.
>
> Dan
>
>
> On 26 Aug 2009, at 01:22, Kyle Lepage wrote:
>
>> Hi Andres, the structure,
>>
>> raw = fiff_setup_read_raw()
>>
>> contains the channel names in raw.info.ch_names
>>
>> For agnostic labeling these names designate left hemisphere and
>> right hemisphere using 'lh' and 'rh'.  For this case the first
>> half of the channels correspond to the left hemisphere and the
>> last half to the right hemisphere.
>>
>> Best regards,
>>
>>  Kyle
>>
>>
>> On Tue, 25 Aug 2009, Sarah Steinvorth wrote:
>>
>>>
>>>
>>>
>>> Begin forwarded message:
>>>
>>>> From: "Andres Felipe Salazar Gomez" <asalazar at nmr.mgh.harvard.edu>
>>>> Date: August 25, 2009 6:29:31 PM EDT
>>>> To: "Daniel G. Wakeman" <dgwakeman at gmail.com>
>>>> Cc: mne_analysis at nmr.mgh.harvard.edu
>>>> Subject: Re: [Mne_analysis] Plotting power spectra of estimates on
>>>> mne_analyze
>>>>
>>>
>>>> Thank you Dan,
>>>>
>>>> I got the power spectrum in source space (in matlab, after
>>>> getting the
>>>> estimates).
>>>> My problem was that since I used matlab, I did not know which set of
>>>> the
>>>> calculated power spectra belonged to either the left or the right
>>>> group of
>>>> vertices (for left and right hemispheres).
>>>>
>>>> It seems the first half of results belongs to the left hemisphere
>>>> and the
>>>> second to the right one.
>>>> Is this correct?
>>>>
>>>> Thanks for your comments,
>>>>
>>>> -- Andrés
>>>>
>>>>
>>>>> Hi Andres,
>>>>>
>>>>> I'm not sure what you mean by "way to link channels and vertices."
>>>>>
>>>>> This seems to suggest you created your power spectrum in sensor
>>>>> space. Is this true?
>>>>>
>>>>> If so what did you use the forward matrix for?
>>>>>
>>>>> If you got the power spectrum values in source space (using some
>>>>> inverse
>>>> solution), then the solution to your problem is easy. Just use
>>>> one of
>>>> the functions below to write those values to either a w file or stc
>>>> file.
>>>>>
>>>>> Dan
>>>>> On 25 Aug 2009, at 21:44, Andres Felipe Salazar Gomez wrote:
>>>>>
>>>>>> Hi MNE users,
>>>>>> I want to plot on mne_analyze the power spectrum values of a
>>>>>> set of
>>>> estimates obtained from a raw file. I got  the estimates in matlab
>>>> using
>>>>>> the forward matrix, the raw file and the noise covariance matrix
>>>>>> but I
>>>> have not been able to create a file that mne_analyze can load and
>>>> plot
>>>> on
>>>>>> the cortex.
>>>>>> I understand mne_write_stc_file (although this one seems to be for
>>>>>> time
>>>>>> domain files) or mne_write_w_file can help me but I am not sure
>>>>>> how to use
>>>>>> them since I do not have a way to link channels and vertices.
>>>>>> Thank you very much for your help,
>>>>>> --
>>>>>> Andres F. Salazar
>>>>>> Research Technologist
>>>>>> Neuroscience Statistics Research Laboratory
>>>>>> asalazar at nmr.mgh.harvard.edu
>>>>>> 149 13th Street, Room 4005
>>>>>> Charlestown, MA  02129
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Andres F. Salazar
>>>> Research Technologist
>>>> Neuroscience Statistics Research Laboratory
>>>> asalazar at nmr.mgh.harvard.edu
>>>> 149 13th Street, Room 4005
>>>> Charlestown, MA  02129
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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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>
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>


-- 
Andres F. Salazar
Research Technologist
Neuroscience Statistics Research Laboratory
asalazar at nmr.mgh.harvard.edu
149 13th Street, Room 4005
Charlestown, MA  02129



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