Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me. It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.eduwrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
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.
Does the aseg label that as ventricle?
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me. It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote: Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is no aseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me. It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote: Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller < sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the original
wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu
wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then
it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and
the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found
the
surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location.
It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is
not
a solution, apparently.
Thank you.
Yang
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
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is no aseg for that. I would love to be corrected on that point though.Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me. It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote: Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the original
wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edu
khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then
it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and
the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I
found the
surface doesn't follow the white matter segmentation closely, although
I
have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both
the
green and yellow sufaces includes a lot of gray matter at the location.
It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white
matter
pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is
not
a solution, apparently.
Thank you.
Yang
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
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller sebastian.moeller1@rwth-aachen.de wrote: Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is no aseg for that. I would love to be corrected on that point though.Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me. It is strange that even the green surface doesn't follow the original wm.mgz, though the wm.mgz as attached in the previous email has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen khoa@nmr.mgh.harvard.edu wrote: Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is, then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and the pial surfaces (red). But I am not very sure of which volume I should work on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it corrected some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I found the surface doesn't follow the white matter segmentation closely, although I have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both the green and yellow sufaces includes a lot of gray matter at the location. It is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white matter pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points is not a solution, apparently.
Thank you.
Yang
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Hi Bruce,
I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu < liu.yang76@gmail.com liu.yang76@gmail.com> wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.desebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.comliu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the original
wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edukhoa@nmr.mgh.harvard.edu
khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is,
then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and
the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I
found the
surface doesn't follow the white matter segmentation closely, although
I
have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both
the
green and yellow sufaces includes a lot of gray matter at the
location. It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white
matter
pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points
is not
a solution, apparently.
Thank you.
Yang
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/compliancelinehttp://www.partners.org/complianceline
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/compliancelinehttp://www.partners.org/complianceline
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Hi Yang,
if you send us the surfaces and the wm.mgz/brainmask.mgz we'll take a look. You need to find the reason for the topological defect in the wm.mgz. By defition to correct a defect the orig (green) surface can no longer follow the boundary of the wm.mgz. If it did it would have a defect! You can also look at the orig.nofix and/or the inflated.nofix to see where the defect is in that region
cheers Bruce
On Tue, 11 Jan 2011, Yang Liu wrote:
Hi Bruce,
I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu < liu.yang76@gmail.com liu.yang76@gmail.com> wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.desebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.comliu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You can
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the original
wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edukhoa@nmr.mgh.harvard.edu
khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is,
then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow) and
the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should be edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I
found the
surface doesn't follow the white matter segmentation closely, although
I
have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both
the
green and yellow sufaces includes a lot of gray matter at the
location. It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white
matter
pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points
is not
a solution, apparently.
Thank you.
Yang
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/compliancelinehttp://www.partners.org/complianceline
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/compliancelinehttp://www.partners.org/complianceline
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
You can also run defect-seg to create segementations and annotations of the defects. This can be quite handy when tracking down defects. Run it with --help to get info on how to use it.
doug
Bruce Fischl wrote:
Hi Yang,
if you send us the surfaces and the wm.mgz/brainmask.mgz we'll take a look. You need to find the reason for the topological defect in the wm.mgz. By defition to correct a defect the orig (green) surface can no longer follow the boundary of the wm.mgz. If it did it would have a defect! You can also look at the orig.nofix and/or the inflated.nofix to see where the defect is in that region
cheers Bruce
On Tue, 11 Jan 2011, Yang Liu wrote:
Hi Bruce,
I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu> wrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu < liu.yang76@gmail.com liu.yang76@gmail.com> wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.desebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there is noaseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.comliu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
> Hi Khoa, > > Thanks for your reply. > I attached the snapshot of the same slice with brainmask.mgz. You can >
see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
> It is strange that even the green surface doesn't follow the original >
wm.mgz, though the wm.mgz as attached in the previous email
> has very well defined boundaries near the wrong regions. > Any idea to correct this? > > > Yang > > > On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen <khoa@nmr.mgh.harvard.edukhoa@nmr.mgh.harvard.edu >
khoa@nmr.mgh.harvard.edu> wrote:
> Hi Yang, > > To edit the pial surface, you want to use brainmask.mgz. > > As for the wm.mgz, you're right in that control points isn't the >
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
> Is the area you pointed out by any chance the ventricle? If it is, >
then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
> On Mon, 10 Jan 2011, Yang Liu wrote: > > Hi Freesurferers, > > I am correcting some defects in the white matter surface (yellow) and >
the
> pial surfaces (red). But I am not very sure of which volume I should >
work
> on. > I did several experiments on editing one volume at a time. > > For pial (the red) surface, I edited brain.mgz first. I found it >
corrected
> some pial defects. > However, I found one previous post here said the volume that should be > edited is brainmask.mgz. > So the second time I only changed brainmask.mgz. It also works. > > So, which one should I work on? > > brian.mgz or brainmask.mgz? > > Also, for defects on the white matter surface (the yellow one), I >
found the
> surface doesn't follow the white matter segmentation closely, although >
I
> have a good wm.mgz. (see attached image). > At the location pointed by the red arrow in the attached image, both >
the
> green and yellow sufaces includes a lot of gray matter at the >
location. It
> is strange that the wm.mgz has a very well defined slice in that > neighborhood. > I am familiar with situations where the surfaces miss a few white >
matter
> pixels, for which I can add a few control points to improve it. > > How shall I edit wm.mgz to correct this? Adding more control points >
is not
> a solution, apparently. > > Thank you. > > Yang > > > > 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 >
> contains patient information, please contact the Partners Compliance >
HelpLine at
> http://www.partners.org/compliancelinehttp://www.partners.org/complianceline >
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. > > > <wrong_surfs_c39.jpg> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu >
Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/compliancelinehttp://www.partners.org/complianceline
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
thank for your suggestion. I will give it a try.
Yang
On Tue, Jan 11, 2011 at 10:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
You can also run defect-seg to create segementations and annotations of the defects. This can be quite handy when tracking down defects. Run it with --help to get info on how to use it.
doug
Bruce Fischl wrote:
Hi Yang,
if you send us the surfaces and the wm.mgz/brainmask.mgz we'll take a look. You need to find the reason for the topological defect in the wm.mgz. By defition to correct a defect the orig (green) surface can no longer follow the boundary of the wm.mgz. If it did it would have a defect! You can also look at the orig.nofix and/or the inflated.nofix to see where the defect is in that region
cheers Bruce
On Tue, 11 Jan 2011, Yang Liu wrote:
Hi Bruce,
I followed the tutorial at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits.
But I couldn't find similar examples as mine in the tutorial. I don't really understand why don't the yellow and green surfaces follow the boundary of wm.mgz, especially the boundary is well defined in the slices.
Yang
On Mon, Jan 10, 2011 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Not without scrolling through the wm volume. You will need to edit it. Have you done the troubleshooting tutorial?
On Jan 10, 2011, at 10:48 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl << fischl@nmr.mgh.harvard.edu> fischl@nmr.mgh.harvard.edu> wrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu < liu.yang76@gmail.com liu.yang76@gmail.com> wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller << sebastian.moeller1@rwth-aachen.de>sebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
> Does the aseg label that as ventricle? > > This pretty much looks like macaque data, so I think there is no aseg for that. I would love to be corrected on that point though.
Best Sebastian
> > On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.com< > liu.yang76@gmail.com> > > liu.yang76@gmail.com> wrote:
> Hi Khoa, >> >> Thanks for your reply. >> I attached the snapshot of the same slice with brainmask.mgz. You >> can >> >> > see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
> It is strange that even the green surface doesn't follow the original >> >> > wm.mgz, though the wm.mgz as attached in the previous email
> has very well defined boundaries near the wrong regions. >> Any idea to correct this? >> >> >> Yang >> >> >> On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen << >> khoa@nmr.mgh.harvard.edu>khoa@nmr.mgh.harvard.edu >> >> > khoa@nmr.mgh.harvard.edu> wrote:
> Hi Yang, >> >> To edit the pial surface, you want to use brainmask.mgz. >> >> As for the wm.mgz, you're right in that control points isn't the >> >> > solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
> Is the area you pointed out by any chance the ventricle? If it is, >> >> > then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
> On Mon, 10 Jan 2011, Yang Liu wrote: >> >> Hi Freesurferers, >> >> I am correcting some defects in the white matter surface (yellow) >> and >> >> > the
> pial surfaces (red). But I am not very sure of which volume I should >> >> > work
> on. >> I did several experiments on editing one volume at a time. >> >> For pial (the red) surface, I edited brain.mgz first. I found it >> >> > corrected
> some pial defects. >> However, I found one previous post here said the volume that should >> be >> edited is brainmask.mgz. >> So the second time I only changed brainmask.mgz. It also works. >> >> So, which one should I work on? >> >> brian.mgz or brainmask.mgz? >> >> Also, for defects on the white matter surface (the yellow one), I >> >> > found the
> surface doesn't follow the white matter segmentation closely, >> although >> >> > I
> have a good wm.mgz. (see attached image). >> At the location pointed by the red arrow in the attached image, both >> >> > the
> green and yellow sufaces includes a lot of gray matter at the >> >> > location. It
> is strange that the wm.mgz has a very well defined slice in that >> neighborhood. >> I am familiar with situations where the surfaces miss a few white >> >> > matter
> pixels, for which I can add a few control points to improve it. >> >> How shall I edit wm.mgz to correct this? Adding more control points >> >> > is not
> a solution, apparently. >> >> Thank you. >> >> Yang >> >> >> >> 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< >> http://www.partners.org/complianceline%3E >> >> > 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. >> >> >> <wrong_surfs_c39.jpg> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu >> >> > Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer< >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu > > Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer< > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%3E > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 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< > http://www.partners.org/complianceline%3E > > 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. >
>
Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edu moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Hi Yang,
Are the slices before and after this slice the same as this one?
Hi Bruce,
Do you know how to fix it?
Yang
On Mon, Jan 10, 2011 at 10:43 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Then I must be a topologica defect
On Jan 10, 2011, at 10:37 PM, Yang Liu liu.yang76@gmail.com wrote:
Hi Sebastian,
Yes. It is Macaque. There is no aseg.
Yang
On Mon, Jan 10, 2011 at 10:15 PM, Sebastian Moeller <sebastian.moeller1@rwth-aachen.de sebastian.moeller1@rwth-aachen.de> wrote:
Hi All,
On Jan 10, 2011, at 19:12 , Bruce Fischl wrote:
Does the aseg label that as ventricle?
This pretty much looks like macaque data, so I think there isno aseg for that. I would love to be corrected on that point though.
Best Sebastian
On Jan 10, 2011, at 9:34 PM, Yang Liu < liu.yang76@gmail.com
liu.yang76@gmail.com> wrote:
Hi Khoa,
Thanks for your reply. I attached the snapshot of the same slice with brainmask.mgz. You
can see clearly that the green and yellow surface at the wrong regions. They doesn't look like ventricles to me.
It is strange that even the green surface doesn't follow the
original wm.mgz, though the wm.mgz as attached in the previous email
has very well defined boundaries near the wrong regions. Any idea to correct this?
Yang
On Mon, Jan 10, 2011 at 6:16 PM, Khoa Nguyen
<khoa@nmr.mgh.harvard.edu khoa@nmr.mgh.harvard.edu> wrote:
Hi Yang,
To edit the pial surface, you want to use brainmask.mgz.
As for the wm.mgz, you're right in that control points isn't the
solution. Control points are to fix intensity problem, but you can also add wm voxels manually to fix any wm defects. In this case, adding that many control points would probably make the situation worse because the entire area will brighten and that would potentially extend the surfaces to include grey matter.
Is the area you pointed out by any chance the ventricle? If it is,
then it doesn't matter that the white surface includes it. It's hard to tell with just this image. Do you mind sending a snapshot of the brainmask.mgz for this slice?
On Mon, 10 Jan 2011, Yang Liu wrote:
Hi Freesurferers,
I am correcting some defects in the white matter surface (yellow)
and the
pial surfaces (red). But I am not very sure of which volume I should
work
on. I did several experiments on editing one volume at a time.
For pial (the red) surface, I edited brain.mgz first. I found it
corrected
some pial defects. However, I found one previous post here said the volume that should
be
edited is brainmask.mgz. So the second time I only changed brainmask.mgz. It also works.
So, which one should I work on?
brian.mgz or brainmask.mgz?
Also, for defects on the white matter surface (the yellow one), I
found the
surface doesn't follow the white matter segmentation closely,
although I
have a good wm.mgz. (see attached image). At the location pointed by the red arrow in the attached image, both
the
green and yellow sufaces includes a lot of gray matter at the
location. It
is strange that the wm.mgz has a very well defined slice in that neighborhood. I am familiar with situations where the surfaces miss a few white
matter
pixels, for which I can add a few control points to improve it.
How shall I edit wm.mgz to correct this? Adding more control points
is not
a solution, apparently.
Thank you.
Yang
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.
<wrong_surfs_c39.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
-- Sebastian Moeller
telephone: 626-807-5242 / 626-395-6523 / 626-395-6616 fax: 626-395-8826 German GSM: 0 15 77 - 1 90 31 41 US CDMA: + 1 - 626 - 807 - 5242 moeller@caltech.edumoeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Khoa Nguyen -
khoa＠nmr.mgh.harvard.edu
-
Sebastian Moeller -
Yang Liu -
Yang Liu