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.
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?
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
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.
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.