[Mne_analysis] Fwd: coordinates of the stc vertexes?

[Matti Hamalainen]

Here is the resolution. I am sorry it did not go to the mailing list in the first place.

- Matti

Begin forwarded message:

> From: Matti Hamalainen <msh at nmr.mgh.harvard.edu>
> Date: June 9, 2011 2:45:53 PM GMT+03:00
> To: Elena Orekhova <Elena.Orekhova at neuro.gu.se>
> Subject: Re: [Mne_analysis] coordinates of the stc vertexes?
> 
> 
> On Jun 9, 2011, at 2:36 PM, Elena Orekhova wrote:
> 
>> Ok...
>> Does it mean that sources are only positioned in the surface vertexes with low numbers   (up to 10241 in my case) and that higher number vertexes are not used by MNE?
> 
> Hei Elena,
> 
> Yes! The low number vertices are all over the surface. This is what I meant by the "special numbering" but I realized I was not very clear about that. On "normal" subjects the 10242 vertex numbers (after morphing) use the full range. I hope this helps.
> 
> - Matti
> 
> 
>  
>> 
>> Thank you!
>> Elena
>> 
>> 
>> 
>> From: Matti Hamalainen [msh at nmr.mgh.harvard.edu]
>> Sent: Thursday, June 09, 2011 1:12 PM
>> To: Elena Orekhova
>> Subject: Re: [Mne_analysis] coordinates of the stc vertexes?
>> 
>> 
>> Hi Elena,
>> 
>> On Jun 9, 2011, at 1:41 PM, Elena Orekhova wrote:
>> 
>>> Hi Matti,
>>> Thank you for your reply. Sorry for me being unclear.
>>> 
>>> The number of vertexes in the fsaverage inflated surface of one hemisphere is  163842 and surfs(1).vertno ranges from 1 to  163842.
>>> ([surfs] = mne_read_surfaces('inflated','true','true','true', 'fsaverage')  )
>>> 
>>> The number of vertexes in my fsaverage-morphed stc  file is 10242 and their numbers range from 0 to 10241. So, there is no corresponcence between stc and surfs vertexes.
>>> 
>>> How can I know the nearest fsaverage surface vertex for the stc source?
>>> or 
>>> Is there a direct way to know MNE/Talairach coordinates of the stc vertexes?
>> 
>> I repeat: vertex number 0 in the left hemisphere stc file of fsaverage has data corresponding to vertex number 0 of the fsaverage surface. When you are in matlab, you need to add one to the stc vertex numbers, since the output of mne_read_surfaces numbers the vertices from 1 instead of 0 like the original files do.
>> 
>> In mne_analyze you can inquire the vertex numbers of specific vertices. 
>> 
>>  
>> 
>> 
>> ---------
>> 
>> Matti Hamalainen, Ph.D.
>> Athinoula A. Martinos Center for Biomedical Imaging
>> Massachusetts General Hospital
>> 
>> msh at nmr.mgh.harvard.edu
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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