[Mne_analysis] Error mne_surf2bem

Laetitia Grabot laetitia.grabot at gmail.com
Wed Jan 13 10:04:01 EST 2016
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Dear MNE-users,

I have a problem for two of my subjects when creating the high resolution
head surface with mne_surf2bem (after creating the BEM surfaces). The error
I get is the following one. When I look to the outer_skin.fif, everything
looks ok. What is the problem and what could be a solution?

Thanks!
Laetitia G.

Command:
mne_surf2bem --surf ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.seghead --id 4
--check --force --fif ${SUBJECTS_DIR}/${SUBJECT}/bem/${SUBJECT}-head.fif

Output:
mne_surf2bem version 1.8 compiled at Jan 11 2016 04:32:34

input  file #   1 :
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//cc150418/surf/lh.seghead
/ id = 4 / sigma N/A
output file       :
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//cc150418/bem/cc150418-head.fif

New quad file : nvert = 202887 nquad = 203438
    Triangle and vertex normals and neighboring triangles...[done]
    Vertex neighbors...    Warning: Too many neighbors for vertex 107343
    Warning: Too many neighbors for vertex 107345
    Warning: Too many neighbors for vertex 107347
    Warning: Too many neighbors for vertex 108287
    Warning: Too many neighbors for vertex 108289
    Warning: Too many neighbors for vertex 109198
    Warning: Too many neighbors for vertex 109200
    Warning: Too many neighbors for vertex 124522
    Warning: Too many neighbors for vertex 125455
    Warning: Too many neighbors for vertex 125456
    Warning: Too many neighbors for vertex 131243
    Warning: Too many neighbors for vertex 131245
    Warning: Too many neighbors for vertex 132243
    Warning: Too many neighbors for vertex 132245
[done]
    Distances between neighboring vertices...[1219568 distances done]
    Warning: 8 topological defects were fixed.
    Warning: 985 vertices had incorrect number of distinct neighbors
(fixed).
valid = 1  # volume info valid
filename =
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//cc150418/mri/seghead.mgz
volume = 256 256 256
voxelsize = 1.0000 1.0000 1.0000
xras   = -1.0000 0.0000 0.0000
yras   = 0.0000 0.0000 -1.0000
zras   = 0.0000 1.0000 0.0000
cras   = -0.5000 22.2651 -13.4940
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//cc150418/surf/lh.seghead
read. id = 4

outer skin  CM is  -3.64  -8.94  -9.34 mm
Surface outer skin  is not complete (sum of solid angles = 0.999986 * 4*PI
instead).
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