# map between sources and voxels

**URL:** <https://mne.discourse.group/t/map-between-sources-and-voxels/186>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [December 3, 2009, 4:31pm UTC](https://mne.discourse.group/t/map-between-sources-and-voxels/186 "2009-12-03T16:31:06Z")\
**Posts on this page:** 2\
**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:** [December 3, 2009, 4:31pm UTC](https://mne.discourse.group/t/map-between-sources-and-voxels/186/1 "2009-12-03T16:31:06Z")

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Hello all,

Thank you again for the good discussing on that previous issue. Now I  
have a more MNE-specific question.

Suppose I run compute\_mne\_raw\_inverse using a single label (e.g.  
cortex-lh.label), and then convert the output of that function to  
a .mat file using mne\_raw2mat. In the resulting .mat file I see a  
[channels] by [time] matrix with data, which makes sense. Judging by  
the number of channels, I imagine they map to the sources within that  
label, and not the vertices. Then, in the info structure there are  
names for all these channels, and if I understand it correctly that  
contains the number of the vertex that the source maps to. In that  
case, is there a 1-1 relationship between sources and vertices? That  
would mean that there's an awful lot of quiet voxels in the results  
(e.g. given the ~3000 sources I get in the left hemisphere, using 7mm  
spacing, and 160K vertices being indexed). Shouldn't a given source  
affect more than one vertex in the brain, if the triangles are small  
enough?

I guess my question boils down to the definition and relationship  
between vertices and sources. Please let me know if I'm mistaken in my  
line of thought.

Thanks,

Gus

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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:** [December 3, 2009, 4:44pm UTC](https://mne.discourse.group/t/map-between-sources-and-voxels/186/2 "2009-12-03T16:44:18Z")

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Hi Gus,

> Hello all,
> 
> Thank you again for the good discussing on that previous issue. Now I  
> have a more MNE-specific question.
> 
> Suppose I run compute\_mne\_raw\_inverse using a single label (e.g.  
> cortex-lh.label), and then convert the output of that function to  
> a .mat file using mne\_raw2mat.

First, the use of mne\_raw2mat is quite unnecessary. You can read the  
signals directly from the fif files with the Matlab routines. This  
saves time and disk space. A good starting point is mne\_ex\_read\_raw.

> In the resulting .mat file I see a  
> [channels] by [time] matrix with data, which makes sense. Judging by  
> the number of channels, I imagine they map to the sources within that  
> label, and not the vertices. Then, in the info structure there are  
> names for all these channels, and if I understand it correctly that  
> contains the number of the vertex that the source maps to. In that  
> case, is there a 1-1 relationship between sources and vertices? That  
> would mean that there's an awful lot of quiet voxels in the results  
> (e.g. given the ~3000 sources I get in the left hemisphere, using 7mm  
> spacing, and 160K vertices being indexed). Shouldn't a given source  
> affect more than one vertex in the brain, if the triangles are small  
> enough?
> 
> I guess my question boils down to the definition and relationship  
> between vertices and sources. Please let me know if I'm mistaken in my  
> line of thought.

Anyhow, in the info structure contained in the mat file output by  
mne\_raw2mat there is a field ch\_lognos which contains the vertex  
numbers of the sources in the densely triangulated surface. There is  
the logno field in the channel descriptors if you load the fif file  
directly.

For visualization and morphing MNE uses a "spreading operator" to fill  
in values to all vertices. This is discussed in section 8.3 of the MNE  
manual.

- Matti