[Mne_analysis] mne_volume_source_space output

Tavabi, Kambiz TAVABIK at email.chop.edu
Wed Jul 14 12:12:25 EDT 2010
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I need the (sparse) interpolation matrix which allows mne_volume_data2mri to create an MRI overlay file. I am trying to create that matrix using volumetric source space using mne_volume_source_space --mri, the following terminal commands:
(1) mne_volume_source_space --mri mrfile.mgz --src subjectsVolSrc.fif
(2) mne_volume_source_space --bem subjects-5120-bem.fif --surf subjects-lh.inflated  --mri subjects.mgz --src subjectsVolSrc.fif
Result in an output ending with: "Setting up interpolation...No nonzero elements specified". No output file is given. What elements does the program require? And how do I provide them?
Also, am I using subjects surface and bem files correctly with this program? The two files were produced during the mne_make_source_space routine.
Does mne_volume_source_space take into account both hemisphere surfaces with --surf subjects-lh.inflated, or am I supposed to run it twice? Thanks for your time.

FYI the initial portion of the terminal output is as follows:
Boundary surface file : /MEG_Lab/tavabik/CBU/clk/mne/subjects/s0149/surf/lh.inflated
Output file           : /MEG_Lab/tavabik/CBU/clk/mne/subjects/s0149/src/VolSrcSpace_149
grid                  : 5.0 mm
mindist               : 5.0 mm
MRI volume            : /MEG_Lab/tavabik/CBU/clk/mne/subjects/s0149/mri/orig/001.mgz

Triangle file : created by dw01 on Mon Jun  2 05:09:29 2008 nvert = 129315 ntri = 258626
        Triangle and vertex normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[775878 distances done]
Loaded bounding surface from /MEG_Lab/tavabik/CBU/clk/mne/subjects/s0149/surf/lh.inflated (129315 nodes)
Surface CM = (   4.4  -10.1   -1.6) mm
Surface fits inside a sphere with radius  140.0 mm
Surface extent:
        x =  -48.3 ...   48.3 mm
        y = -127.9 ...  127.9 mm
        z =  -71.2 ...   71.2 mm
Grid extent:
        x =  -50.0 ...   50.0 mm
        y = -130.0 ...  130.0 mm
        z =  -75.0 ...   75.0 mm
34503 sources before omitting any.
32539 sources after omitting infeasible sources.
Source spaces are in MRI coordinates.
Checking that the sources are inside the bounding surface and at least    5.0 mm away (will take a few...)
21854 source space points omitted because they are outside the inner skull surface.
2849 source space points omitted because of the    5.0-mm distance limit.
Thank you for waiting.
7836 sources remaining after excluding the sources outside the surface and less than    5.0 mm inside.
Adjusting the neighborhood info...[done]
Reading /MEG_Lab/tavabik/CBU/clk/mne/subjects/s0149/mri/orig/001.mgz...[done]

Kambiz Tavabi PhD
Biomedical Imaging Laboratory
The Children's Hospital of Philadelphia
34th Street and Civic Center Boulevard
Philadelphia, Pa. 19104
Tel: 267.426.0302
email: tavabik at email.chop.edu

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