[Mne_analysis] creating source space incomplete

Maria Felber felber at cbs.mpg.de
Mon Aug 20 07:39:31 EDT 2012
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Dear all,

I ran a script, to create my bem with the following options:
mne_setup_bem.sh im18 --icosrc 3 --icovol 2 --bem 3 translated to oct-6, 5120 points per layer and 3 compartments

It ran completely through and did not give me any visible error messages. However, the process did not create the file, I used so far for any other subject. 
The file I am looking for is: freesurfer/im18/bem/im18-oct-6p-src.fif

Here is the screen output of this process:

Running: mne_setup_bem.sh im18 --icosrc 3 --icovol 2 --bem 3
mne_setup_source_space --subject im18 --ico -6 --cps --overwrite

Setting up the source space with the following parameters:

SUBJECTS_DIR = /SCR4/charlie/imesapp/freesurfer/
Subject      = im18
Surface      = white
Octahedron subdivision grade 6
Create a source space with patch information

>>> 1. Creating the source space file /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif...

mne_make_source_space version 2.5 compiled at Jan  6 2011 02:25:18

Loading /SCR4/charlie/imesapp/freesurfer//im18/surf/lh.white...
Triangle file : created by felber on Thu Feb  9 17:52:24 2012 nvert = 146216 ntri = 292428
        Triangle and vertex normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[877284 distances done]
Doing the octahedral vertex picking...
Loading geometry from /SCR4/charlie/imesapp/freesurfer//im18/surf/lh.sphere...
Triangle file : created by felber on Thu Feb  9 19:55:04 2012 nvert = 146216 ntri = 292428
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[24576 distances done]
Mapping lh im18 -> oct (6) ...[done]
Setting up the triangulation for the decimated surface...
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[24576 distances done]
loaded lh.white 4098/146216 selected to source space (oct = 6)

Loading /SCR4/charlie/imesapp/freesurfer//im18/surf/rh.white...
Triangle file : created by felber on Thu Feb  9 21:13:21 2012 nvert = 148888 ntri = 297772
        Triangle and vertex normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[893316 distances done]
Doing the octahedral vertex picking...
Loading geometry from /SCR4/charlie/imesapp/freesurfer//im18/surf/rh.sphere...
Triangle file : created by felber on Thu Feb  9 23:13:48 2012 nvert = 148888 ntri = 297772
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[24576 distances done]
Mapping rh im18 -> oct (6) ...[done]
Setting up the triangulation for the decimated surface...
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[24576 distances done]
loaded rh.white 4098/148888 selected to source space (oct = 6)

Wrote /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif
You are now one step closer to computing the gain matrix.

>>> 2. Creating ASCII versions for checking with MRI lab...

Reading from /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif...
Read 2 source spaces from /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif with a total of 8196 source locations
Selection triangulation information is available.
Source spaces are now in MRI (surface RAS) coordinates.
Wrote /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-lh.dip
Wrote /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-rh.dip
Wrote /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-lh.pnt
Wrote /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-rh.pnt
        Wrote 4098 vertices into /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-lh.w
        Wrote 4098 vertices into /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-rh.w
Temporary files removed.

>>> 3. Creating a source space with patch information
       This will take quite a while...

mne_add_patch_info version 1.6 compiled at Jan  6 2011 02:25:26

input file                : /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif
output file               : /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6p-src.fif
output w file stem        : /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6p

Reading from /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif...
Loaded 2 source spaces from /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[877284 distances done]
        Triangle normals and neighboring triangles...[done]
        Vertex neighbors...[done]
        Distances between neighboring vertices...[893316 distances done]
Defining patches (this will take a few mins)...
Node 61 does not belong to any of the patches

Finished.

The file /SCR4/charlie/imesapp/freesurfer//im18/bem/im18-oct-6-src.fif does exist. Has anyone an idea what went wrong and how to solve this problem?
Thank you.
Cheers,
Maria Felber



-- 
Maria J. Felber, PhD Student
Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstraße 1A 
04103 Leipzig, Germany
Phone:  +49 341 9940-2465/2522




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