[Mne_analysis] Error mne_surf2bem

[Laetitia Grabot]

2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:

> 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.
>
>

Outer_skin.fif is created by the mne_flash_bem command, but I guess it is
used by mne_surf2bem, isn't it?



> >
> > 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.
>
>
I want to create this high resolution head to read it with mne_analyze and
do my coregistration (and it worked well with my other subjects). What is
the difference between lh.seghead and lh.smseghead (by the way, I don't
have any lh.smseghead file in the surf directory of my subjects)?
More concretely how can I edit the volume as you suggested?


> hth
> d
>
>
Thanks Denis!


> >
> > 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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