[Mne_analysis] Error mne_surf2bem

[dgw]

Hi Laetitia,

Please see my replies in text:

On Wed, Jan 13, 2016 at 10:04 AM, Laetitia Grabot
<laetitia.grabot at gmail.com> wrote:
> 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?

The outer_skin.fif is not created by any of these commands.

>
> 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

This looks odd to me. Why are you trying to make lh.seghead?
typically, if you want to make a high resolution head surface you use
lh.smseghead. First, check this suggestion. Then, if you still have a
problem, occasionally editing the volume to make the neck for example
a smooth white area 2 slices thick, then re-running mkheadsurf.

hth
d

>
> 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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