creating source space incomplete

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1

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

2

Hi Maria,

mne_setup_bem.sh is not a default MNE command so it's not clear
to me what can go wrong. Can you try on the MNE sample data to see
if the problem occurs too. If not then it's a problem with your subject
otherwise I should be able to reproduce the bug and look into it.

Do you hesitate to share this mne_setup_bem.sh script as I feel it could be
useful to others.

Best,
Alex

3

Hi Alex,

though it must sound like a stupid question: what sample data do you mean and where can I get it?
About the shell-script: it is not mine and it works with a Makefile-script in the background, making it rather difficult to deciphere, what the program is supposed to do at all times. I should be able, to give you the exact mne command lines and options by tomorrow.
About sharing the script itself, I have to ask, as it is not mine.
Cheers,
Maria

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4

hi Maria,

your problem seem to occur with only one of your subjects so forget about the
sample data. Share the files with us so we can investigate.

Best,
Alex