[Mne_analysis] Error mne_surf2bem
Laetitia Grabot
laetitia.grabot at gmail.com
Wed Jan 13 11:30:47 EST 2016
The version of freesurfer I use:
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
I run exactly this command (SUBJET being the identification number of my
subject):
mkheadsurf -s ${SUBJECT}
And I got:
INFO: log file is
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/scripts/mkheadsurf.log
--------------------------------
mercredi 13 janvier 2016, 17:20:14 (UTC+0100)
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/raw
mri_seghead --invol
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/mri/T1.mgz
--outvol
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/mri/seghead.mgz
--fill 255 --thresh1 20 --thresh2 20 --nhitsmin 2
--------------------------------
input volume:
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/mri/T1.mgz
output volume:
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/mri/seghead.mgz
threshold1: 20
threshold2: 20
nhitsmin: 2
fill value: 255
Loading input volume
Filling Columns
Filling Rows
Filling Slices
Merging and Inverting
Growing
Counting
N Head Voxels = 4152415
N Back Voxels = 12624801
Avg. Back Intensity = 1.873793
Writing output
Done
--------------------------------
mercredi 13 janvier 2016, 17:20:23 (UTC+0100)
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/raw
mri_tessellate
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/mri/seghead.mgz
255
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead
--------------------------------
$Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $
$Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
slice 20: 1948 vertices, 2084 faces
slice 30: 9920 vertices, 10146 faces
slice 40: 20273 vertices, 20656 faces
slice 50: 34962 vertices, 35510 faces
slice 60: 52931 vertices, 53483 faces
slice 70: 65372 vertices, 65913 faces
slice 80: 76493 vertices, 77128 faces
slice 90: 88516 vertices, 89255 faces
slice 100: 101315 vertices, 102093 faces
slice 110: 113690 vertices, 114530 faces
slice 120: 125408 vertices, 126220 faces
slice 130: 136601 vertices, 137466 faces
slice 140: 147417 vertices, 148287 faces
slice 150: 157862 vertices, 158732 faces
slice 160: 167342 vertices, 168191 faces
slice 170: 176668 vertices, 177506 faces
slice 180: 186488 vertices, 187323 faces
slice 190: 196817 vertices, 197657 faces
slice 200: 209603 vertices, 210484 faces
slice 210: 222573 vertices, 223399 faces
slice 220: 227457 vertices, 228130 faces
slice 230: 228785 vertices, 229419 faces
slice 240: 228810 vertices, 229434 faces
slice 250: 228810 vertices, 229434 faces
using the conformed surface RAS to save vertex points...
writing
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead
using vox2ras matrix:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
--------------------------------
mercredi 13 janvier 2016, 17:20:26 (UTC+0100)
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/raw
mris_smooth -n 10 -b area.seghead -c curv.seghead
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead
--------------------------------
smoothing for 10 iterations
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
writing smoothed curvature to
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.curv.seghead
writing smoothed area to
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.area.seghead
--------------------------------
mercredi 13 janvier 2016, 17:20:33 (UTC+0100)
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/raw
mris_inflate -n 10 -sulc sulc.seghead
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead.inflated
--------------------------------
niterations = 10
sulc name = sulc.seghead
avg radius = 103.0 mm, total surface area = 151855 mm^2
writing inflated surface to
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.seghead.inflated
writing sulcal depths to
/neurospin/meg/meg_tmp/Rabbit_LaetitiaG_2015/freesurfer_segmentation//lb140113/surf/lh.sulc.seghead
step 060: RMS=0.029 (target=0.015)
inflation complete.
inflation took 0.8 minutes
Started at: mercredi 13 janvier 2016, 17:20:14 (UTC+0100)
Ended at: mercredi 13 janvier 2016, 17:21:22 (UTC+0100)
mkheadsurf done
2016-01-13 17:24 GMT+01:00 dgw <dgwakeman at gmail.com>:
> 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).
> >> >> >
> >> >> > _______________________________________________
> >> >> > 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
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> >> >> > you
> >> >> > in
> >> >> > error
> >> >> > but does not contain patient information, please contact the sender
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> >> >> > dispose of the e-mail.
> >> >> >
> >> >> _______________________________________________
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> >> >
> >> >
> >> >
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> >> > contains patient information, please contact the Partners Compliance
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> >
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> >
> >
> > 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
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> > but does not contain patient information, please contact the sender and
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