[Mne_analysis] Format of MATLAB mne_read_stc_file output

Eric Larson larson.eric.d at gmail.com
Sat Aug 10 16:57:17 EDT 2013
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Hey Steve,

Once you morph the individual subject's data to the average brain
"fsaverage", the source space points in the STC will correspond to those in
fsaverage's source space, which is usually the standard grade-5 decimation
with 10242 vertices per hemisphere. The vertices used in fsaverage are
conveniently just the first 10242 vertices in each hemisphere (1:10242 in
1-based indexing). Read fsaverage's source space and it should make sense.
If on the other hand you morphed to some other average brain (not
fsaverage), the vertices might correspond to some other set of indices, but
they probably still correspond to a grade-5 decimation.

Cheers,
Eric



On Sat, Aug 10, 2013 at 1:50 PM, Stephen Politzer-Ahles <
politzerahless at gmail.com> wrote:

> Hello,
>
> I am looking for some clarification on the format of the output of
> mne_read_stc_file.m . For example, when I run it on one of my files (a left
> hemisphere .stc file which was computed morphed to an average brain), I get
> a file with 10242 vertices:
>
>         tmin: -0.8000
>        tstep: 0.0017
>     vertices: [10242x1 uint32]
>         data: [10242x780 double]
>
> However, when I read the source space that corresponds to this .stc file
> (a source space that was made using --ico 4), it only has 2562 source
> vertices per hemisphere (from src(1).vertno):
>
>               id: 101
>               np: 163842
>             ntri: 327680
>      coord_frame: 5
>               rr: [163842x3 double]
>               nn: [163842x3 double]
>             tris: [327680x3 int32]
>             nuse: 2562
>            inuse: [1x163842 int32]
>           vertno: [1x2562 int32]
>         nuse_tri: 5120
>         use_tris: [5120x3 int32]
>          nearest: []
>     nearest_dist: []
>            pinfo: []
>             dist: []
>       dist_limit: []
>
> So basically I am just not sure what the 10242 vertices read from my .stc
> file correspond to, as that number doesn't correspond to anything I see in
> the source space. Based on my reading of lines 40-45 of
> mne_label_time_courses.m, it looks to me like the first 2562 vertices in
> the stc file correspond to the actual vertices from my source space,
> whereas the rest are ignored --- is that true?  (The reason I am interested
> in this is because rather than reading in label time courses, I want to try
> reading in just the time courses that correspond to the used vertices in
> the source space, and then use the triangle information from src.use_tris
> and src.tris to identify source vertices that are adjacent to each other
> for the purpose of spatio-temporal clustering. In that case, would
> stc.data( source(1).vertno, : )  be the way to get just the timecourses
> corresponding to source vertices?)
>
> Thank you,
> Steve
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Psychology Department
> http://files.nyu.edu/spa268/public
>
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