[Mne_analysis] plotting from MATLAB

[Gustavo Sudre]

Thank you Matti and Pavan. That does help.

Just to make it clear, if I do it the old way I was doing it, by  
opening the source localization results I get from raw2mat in matlab,  
and later writing a .stc file with that information, it should work  
properly, correct? For the vertices argument to write .stc, I used the  
information in MNE_raw_info.ch_names.

Gus

On Sep 21, 2009, at 7:42 AM, Matti Hamalainen wrote:

>
> On Sep 21, 2009, at 7:09 AM, Pavan Ramkumar wrote:
>
>> Hi Gus,
>>
>>> plot the results in MATLAB? If so, do I just assume the results for
>>> the vertices not present in the info structure to be zero?
>>>
>>
>> If I understand correctly, your assumption would be right for a  
>> smoothing
>> level (# smooth steps) of 0. If not you may need to precompute your
>> smoothing matrices as described in section 8.3 of the manual. I  
>> think the
>> neighborhood information of the vertices can be computed from their
>> coordinates if you calculated your source space with the '--cps'  
>> option.
>>
>> I'm not sure if there is an easier way but I may be wrong on this.  
>> If you
>> do find out please let me know.
>
> Hi Gus,
>
> Unfortunately, the neighborhood information is never in the source  
> space files, you need to recompute it. Besides, you usually want to  
> visualize the data on a surface other than the one in the source  
> space file. You can start by loading the inflated surfaces
>
> s = mne_read_surfaces('inflated',true,true,true,'sample',getenv 
> ('SUBJECTS_DIR'),true);
>
> Then you need to look at the tris member of each surface returned  
> and figure out the neighboring vertices.
>
> I hope this helps
>
> - Matti
>
>
>
>
>
>
>
>
> ---------
>
> Matti Hamalainen, Ph.D.
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
>
> msh at nmr.mgh.harvard.edu
>
>
>
>
>
>