[Mne_analysis] Error mne_surf2bem
dgw
dgwakeman at gmail.com
Wed Jan 13 11:24:58 EST 2016
On Wed, Jan 13, 2016 at 11:21 AM, Laetitia Grabot
<laetitia.grabot at gmail.com> wrote:
>
>
> 2016-01-13 17:14 GMT+01:00 dgw <dgwakeman at gmail.com>:
>>
>> 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).
>
>
> Ok, it's getting clearer!
>
>>
>> >
>> >
>> >>
>> >> >
>> >> > 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?
>
>
> Yes, the exact command I've run was (and there was no error message):
>
> mkheadsurf -s ${SUBJECT}
What version of freesurfer are you using? What exact command did you
run and what are the outputs of it?
>
>
>>
>>
>> > 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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