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?
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
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.
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.
2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:
Hi Laetitia,
Please see my replies in text:
> 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?
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).
>
> _______________________________________________
> 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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in
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> but does not contain patient information, please contact the sender and
> properly
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2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:
Hi Laetitia,
Please see my replies in text:
> 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).
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?
2016-01-13 17:14 GMT+01:00 dgw <dgwakeman at gmail.com>:
>
> 2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:
>>
>> Hi Laetitia,
>>
>> Please see my replies in text:
>>
>> > 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.
>
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2016-01-13 17:14 GMT+01:00 dgw <dgwakeman at gmail.com>:
>
> 2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:
>>
>> Hi Laetitia,
>>
>> Please see my replies in text:
>>
>> > 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?
ok, Laetitia, it looks like i am a bit behind in my mkheadsurf
knowledge (and so is the documentation). You are correct, it shouldn't
create a lh.smseghead (previous versions did this). To fix this, you
can do the following (taken from the slightly out of date
documentation in mkheadsurf)
If the final head surface does not
look good enough, this volume can be edited (eg, freeview
$SUBJECTS_DIR/$SUBJECT/mri/seghead.mgz), then mkheadsurf can be re-run
with -noseghead.
So edit the volume, and fill in any holes in the volume (you should
only need to fill in the outer edges (about 2-3voxels deep). it should
be a very quick operation. It is usually a problem in the bottom
(neck) area of the volume.
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
>
> 2016-01-13 16:47 GMT+01:00 dgw <dgwakeman at gmail.com>:
>>
>> Hi Laetitia,
>>
>> Please see my replies in text:
>>
>> > 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).
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
>> > Mne_analysis Info Page
>> >
>> >
>> > 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
>> > MyComplianceReport.com: Compliance and Ethics Reporting . 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
>> Mne_analysis Info Page
>
>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> Mne_analysis Info Page
>
>
> 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
> MyComplianceReport.com: Compliance and Ethics Reporting . 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.
>
_______________________________________________
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Mne_analysis at nmr.mgh.harvard.edu Mne_analysis Info Page
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.
