[Mne_analysis] mapping between the mne and freesurfer vertex labelling systems

[Alexandre Gramfort]

hi,

> One of the toolbox I am using make use of fsaverage but I am not too sure what was used for the other STCs(as they were processed by someone else a while ago). I tried to plug our stc files with a graphical display of the other toolbox and most/all of the activity is mapped on to occipital area  I re-process the raw data again using fsaverage and stcs files got mapped real nicely. I think the problem might be due to different vertex labelling system - our STC files use the MNE labelling system (used by default using the MNE_make_movie command in MNE suite), while I think other one uses the Freesurfer vertex labels right the way through?

MNE labels and vertice numbers (vertno in MNE jargon) are the same as
freesurfer. If the STC has values on the occipital regions then it's
defined on fsaverage.

Hope this helps,
Alex


>  So basically I was looking for a one to one mapping between these vertices systems that will save me lot of time that otherwise would be spent on pre-processing all our data. I have copied STC files (both new and old) and some images on to the dropbox (if you want to see them). https://www.dropbox.com/sh/7vzdxvt6gq38771/k7XvSdOBkX
>
> Kind Regards,
> Fawad
>
> ______
>
> Dr. Fawad Jamshed
> Neurolex, Department of Psychology,
> University of Cambridge,
> Downing Street, Cambridge CB2 3EB, UK.
> Phone: +44 (0)1223 764 288
> Email: fj247 at cam.ac.uk
> Web: www.neurolex.psychol.cam.ac.uk/directory/fj247 at cam.ac.uk
> ______
>
>
> -----Original Message-----
> From: dgw [mailto:dgwakeman at gmail.com]
> Sent: 07 March 2014 19:03
> To: Fawad Jamshed
> Cc: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] mapping between the mne and freesurfer vertex labelling systems
>
> Hi Fawad,
>
> This depends on what brain these stcs were created. MNE and FreeSurfer use the same vertex labeling. It is possible to create stcs on fsaverage (or even some other common average brain), and have a direct mapping between them. Can you tell us more about the two stc files?
> What brain were they created on an individual in your group or fsaverage? Is that true of both files?
>
> D
>
> On Fri, Mar 7, 2014 at 1:56 PM, Fawad Jamshed <fj247 at cam.ac.uk> wrote:
>> Hi,
>>
>> I have received from an external group some STC files that have been
>> created using the vertex labelling system of freesurfer. (i.e.
>> starting from the occipital pole and spiralling toward the front). I
>> want to compare these with our 'in house' results, which use the MNE
>> vertex labelling system ('loose' spirals, with each pass filling in
>> gaps between the spirals for use in different resolutions). I suspect
>> there is a simple mapping between the two vertex labelling systems ..
>> is this the case, and, if so, could someone point me to where I might find it?
>>
>> Any advice/script/literature would be helpful. Thanks in advance.
>>
>>
>>
>> Regards,
>> Fawad
>>
>>
>>
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