[Mne_analysis] Error mne_surf2bem

dgw dgwakeman at gmail.com
Wed Jan 13 13:00:46 EST 2016
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Hi Laetitia,

Yes the neck ones are typically the problem. From the image though, it
looks like you have some serious signal dropout in the face, which
makes registering to the digitizer points very difficult (and this is
the main advantage of the high resolution surface). You may want to
look into getting a better MR sequence/coil which has less face
dropout.

hth
d

On Wed, Jan 13, 2016 at 12:30 PM, Laetitia Grabot
<laetitia.grabot at gmail.com> wrote:
> Apparently, the problem should be due to these holes at the base of the neck
> (even near to the nose, it's not smooth at all) as it is visible in the
> attached snapshot. I still need to master a bit more freeview to fill the
> holes...
> Thanks for the help!
>
> 2016-01-13 17:58 GMT+01:00 Alexandre Gramfort
> <alexandre.gramfort at telecom-paristech.fr>:
>>
>> I've seen the issue in the past and I ended up recompiling MNE with a
>> looser tolerance....
>>
>> that being said you can do this with python with
>>
>> "mne surf2bem" no _
>>
>> and it should work.
>>
>> Alex
>>
>>
>> On Wed, Jan 13, 2016 at 5:05 PM, 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?
>> >
>> >
>> >>
>> >> >
>> >> > 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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