[Mne_analysis] Error mne_surf2bem

dgw dgwakeman at gmail.com
Wed Jan 13 11:14:24 EST 2016
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On Wed, Jan 13, 2016 at 11:05 AM, Laetitia Grabot
<laetitia.grabot at gmail.com> wrote:
>
> 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?

No, it isn't used by mne_surf2bem. Inside the mne_flash_bem script it
calls mne_surf2bem to create it, but it is not used in the procedure
you are talking about (in fact what you want to do is to create a
similar surface, but better to replace 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)?

Let's proceed here first. Have you run mkheadsurf?

> 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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