[Mne_analysis] Format of MATLAB mne_read_stc_file output

Hari Bharadwaj hari at nmr.mgh.harvard.edu
Sat Aug 10 17:00:01 EDT 2013
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Hi Steve,
   The standard fsaverage surface that is included has 10242 vertices per
hemisphere. The stc files do not retain any information about the
original source-space to which those time-courses belong (since they
are just overlays and you could overlay many different things). They
only have vertex numbers and the corresponding time courses (i.e data).
It is upto to the user to pair the right stc file with the right
surface.

HTH,
Hari


On Sat, August 10, 2013 4:50 pm, Stephen Politzer-Ahles 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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> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
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-- 
Hari Bharadwaj
PhD Candidate, Biomedical Engineering,
Boston University
677 Beacon St.,
Boston, MA 02215

Martinos Center for Biomedical Imaging,
Massachusetts General Hospital
149 Thirteenth Street,
Charlestown, MA 02129

hari at nmr.mgh.harvard.edu
Ph: 734-883-5954





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