# mapping between the mne and freesurfer vertex	labelling systems

**URL:** <https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [March 7, 2014, 6:56pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684 "2014-03-07T18:56:49Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [March 7, 2014, 6:56pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684/1 "2014-03-07T18:56:49Z")

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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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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [March 7, 2014, 7:03pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684/2 "2014-03-07T19:03:11Z")

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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

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [March 18, 2014, 12:17pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684/3 "2014-03-18T12:17:01Z")

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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?

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](https://www.dropbox.com/sh/7vzdxvt6gq38771/k7XvSdOBkX)

Kind Regards,  
Fawad

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [March 18, 2014, 9:34pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684/4 "2014-03-18T21:34:18Z")

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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

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [March 24, 2014, 1:32pm UTC](https://mne.discourse.group/t/mapping-between-the-mne-and-freesurfer-vertex-labelling-systems/684/5 "2014-03-24T13:32:45Z")

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Thanks guys I managed to fix this problem by plugging the average brain they  
have used. The problem was different average brain were used by different  
STC files.

Regards,  
Fawad