[Mne_analysis] Error mne_surf2bem

Laetitia Grabot laetitia.grabot at gmail.com
Wed Jan 13 11:21:54 EST 2016
Search archives: 
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}



>
> > 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).
> >> >
> >> > _______________________________________________
> >> > Mne_analysis mailing list
> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >
> >> >
> >> > The information in this e-mail is intended only for the person to whom
> >> > it is
> >> > addressed. If you believe this e-mail was sent to you in error and the
> >> > e-mail
> >> > contains patient information, please contact the Partners Compliance
> >> > HelpLine at
> >> > http://www.partners.org/complianceline . If the e-mail was sent to
> you
> >> > in
> >> > error
> >> > but does not contain patient information, please contact the sender
> and
> >> > properly
> >> > dispose of the e-mail.
> >> >
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20160113/1ffb04e3/attachment-0001.html

More information about the Mne_analysis mailing list