Hello,
We have a volumetric data (mgz file) of a segmented brain region. We want to detect the surface of this segmented brain volume (i.e. deep brain region) and flatten it into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten volumetric data. We wonder if this could be adapted to our data set. Can anyone offer some advice on how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We want to detect the surface of this segmented brain volume (i.e. deep brain region) and flatten it into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten volumetric data. We wonder if this could be adapted to our data set. Can anyone offer some advice on how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we would like to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area and flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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 Younghoon
I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we would like to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area and flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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 Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice how to generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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.
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly well documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice how to generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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 Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the mri_tessellate command?
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly well documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice
how to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if
not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain
area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense
to
flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region)
and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer
some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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.
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.
is Brain_FS.mgz a segmented volume? How much memory do you have on that machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the mri_tessellate command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly well documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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.
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 Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on that machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to
generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly
well
documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice
how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if
not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so
we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain
area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (
fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make
sense to
flatten volumetric structures. We flatten the cortex, which is a
folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region)
and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer
some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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
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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 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.
and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on that machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to generate a surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the mri_tessellate command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to create the surface, then introduce the cut(s) and run mris_flatten -1 on the resulting patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly well documented. You need the -1 flag to tell it to only use that one surface that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut if not more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make sense to flatten volumetric structures. We flatten the cortex, which is a folded 2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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
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contains patient information, please contact the Partners Compliance
HelpLine
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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 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.
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 Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is needed for further steps in my project.
I am considering to project the texture of the segmented brain area (the pixel intensity on the surface of the volumetric data) to the generated surface (vectorized surface). I wonder whether this can be done in a similar way to the way you project fMRI signal to the surface.
Thanks,
Younghoon Kim -- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and the
size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on that machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix” command to
generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
If you have a segmented volume, you can use mri_tessellate to create
the
surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't terribly
well
documented. You need the -1 flag to tell it to only use that one
surface
that you are giving it, and not to assume that the entire FS directory structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl (
fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one cut
if not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric data.
For flattening, we do not care about the interior of the volume, so
we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented brain
area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl (
fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't make
sense to
flatten volumetric structures. We flatten the cortex, which is a
folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain
region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone offer
some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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
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the
contains patient information, please contact the Partners Compliance
HelpLine
at http://www.partners.org/complianceline . If the e-mail was sent to
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and
properly dispose of the e-mail.
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HelpLine at
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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.
sure, you can do that with mri_vol2surf. Basically the initial surface and the final (inflated) surface have the same number of vertices, so the vertex identity is preserved and mri_vol2surf samples values from the volume onto the surface which can then be displayed on any surface configuration (like inflated)
On Tue, 26 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is needed for further steps in my project.
I am considering to project the texture of the segmented brain area (the pixel intensity on the surface of the volumetric data) to the generated surface (vectorized surface). I wonder whether this can be done in a similar way to the way you project fMRI signal to the surface.
Thanks,
Younghoon Kim
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on
that
machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix”
command to generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to
create the
surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't
terribly well
documented. You need the -1 flag to tell it to only use that one
surface
that you are giving it, and not to assume that the entire FS
directory
structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one
cut if not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric
data.
For flattening, we do not care about the interior of the
volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented
brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't
make sense to
flatten volumetric structures. We flatten the cortex, which is
a folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain
region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to
flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone
offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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.
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The information in this e-mail is intended only for the person to
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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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The information in this e-mail is intended only for the person to
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HelpLine at
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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 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 Bruce,
Thanks to your advice, I was able to generate a mgh file using mri_vol2surf, and thus map the texture onto both the inflated and the flattened surfaces.
I wonder whether it is possible to reversely map the vertices on the vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to the voxels in the volumetric file (mgz file), i.e. find the xyz coordinate of each vertex in the frame of reference of the volumetric file (mgz file) used to generate the vectorized surface.
Also, I’ve noticed that the number of the columns in the texture mapping file (i.e. ‘lh.sig.mgh’, the output of mri_vol2surf command), is equal to the number of the vertices on the vectorized surface. I assume that the texture mapping file and the vectorized surface has a one-to-one vertex/column correspondence. If so, I wonder how the texture intensity of each vertex is stored in the texture mapping file and eventually mapped onto the vectorized surface.
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 26, 2016 at 5:51:01 PM, Bruce Fischl (fischl@nmr.mgh.harvard.edu) wrote:
sure, you can do that with mri_vol2surf. Basically the initial surface and the final (inflated) surface have the same number of vertices, so the vertex identity is preserved and mri_vol2surf samples values from the volume onto the surface which can then be displayed on any surface configuration (like inflated)
On Tue, 26 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is
needed
for further steps in my project.
I am considering to project the texture of the segmented brain area (the pixel intensity on the surface of the volumetric data) to the generated surface (vectorized surface). I wonder whether this can be done in a
similar
way to the way you project fMRI signal to the surface.
Thanks,
Younghoon Kim
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on
that
machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix”
command to generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to
create the
surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't
terribly well
documented. You need the -1 flag to tell it to only use that one
surface
that you are giving it, and not to assume that the entire FS
directory
structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one
cut if not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric
data.
For flattening, we do not care about the interior of the
volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented
brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't
make sense to
flatten volumetric structures. We flatten the cortex, which is
a folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain
region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to
flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone
offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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The information in this e-mail is intended only for the person
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HelpLine
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The information in this e-mail is intended only for the person to
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HelpLine at
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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 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.
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 Bruce,
I sent you a message a while ago but have’t received your reply.
I generated a mgh file using mri_vol2surf, and thus mapped the texture that I want to project onto both the inflated and the flattened surfaces.
I wonder whether it is possible to reversely map the vertices on the vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to the voxels in the volumetric file (mgz file), i.e. find the xyz coordinate of each vertex in the frame of reference of the volumetric file (mgz file) used to generate the vectorized surface.
Also, I’ve noticed that the number of the columns in the texture mapping file (i.e. ‘lh.sig.mgh’, the output of mri_vol2surf command), is equal to the number of the vertices on the vectorized surface. I assume that the texture mapping file and the vectorized surface has a one-to-one vertex/column correspondence. If so, I wonder how the texture intensity of each vertex is stored in the texture mapping file and eventually mapped onto the vectorized surface.
Thanks,
Younghoon Kim
-- Younghoon Kim, Dep. of Bio and Brain Engineering, KAIST OMICS Lab ---------------------------------------------- younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
켜짐 2016년 7월 27일 에서 06:51:01, Bruce Fischl (fischl@nmr.mgh.harvard.edu) 작성됨:
sure, you can do that with mri_vol2surf. Basically the initial surface and the final (inflated) surface have the same number of vertices, so the vertex identity is preserved and mri_vol2surf samples values from the volume onto the surface which can then be displayed on any surface configuration (like inflated)
On Tue, 26 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the segmented brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is
needed
for further steps in my project.
I am considering to project the texture of the segmented brain area (the pixel intensity on the surface of the volumetric data) to the generated surface (vectorized surface). I wonder whether this can be done in a
similar
way to the way you project fMRI signal to the surface.
Thanks,
Younghoon Kim
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl (fischl@nmr.mgh.harvard.edu)
wrote:
and 255 is the label that you want to cover? 16G may not be enough. Do you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on
that
machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix”
command to generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to
create the
surface, then introduce the cut(s) and run mris_flatten -1 on the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't
terribly well
documented. You need the -1 flag to tell it to only use that one
surface
that you are giving it, and not to assume that the entire FS
directory
structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me some
advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least one
cut if not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the volumetric
data.
For flattening, we do not care about the interior of the
volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the segmented
brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't
make sense to
flatten volumetric structures. We flatten the cortex, which is
a folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hello,
We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect
the surface of this segmented brain volume (i.e. deep brain
region) and
flatten it
into a 2D image with its original surface texture.
We’ve noticed that Freesurfer supports an algorithm to
flatten
volumetric
data. We
wonder if this could be adapted to our data set. Can anyone
offer some
advice on
how to apply FreeSurfer to this more generic task?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
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.
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.
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
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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.
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
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HelpLine at
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and properly
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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 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.
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 Younghoon
yes, the vertex index is perserved across all the surface and patch representations, so you should always be able to go from a flattened vertex back to its white or pial location
cheers Bruce On Thu, 8 Sep 2016, Younghoon Kim wrote:
Hi Bruce,
I sent you a message a while ago but have’t received your reply.
I generated a mgh file using mri_vol2surf, and thus mapped the texture that I want to project onto both the inflated and the flattened surfaces.
I wonder whether it is possible to reversely map the vertices on the vectorized surface (such as, ‘lh.orig’ or ‘lh.inflate') back to the voxels in the volumetric file (mgz file), i.e. find the xyz coordinate of each vertex in the frame of reference of the volumetric file (mgz file) used to generate the vectorized surface.
Also, I’ve noticed that the number of the columns in the texture mapping file (i.e. ‘lh.sig.mgh’, the output of mri_vol2surf command), is equal to the number of the vertices on the vectorized surface. I assume that the texture mapping file and the vectorized surface has a one-to-one vertex/column correspondence. If so, I wonder how the texture intensity of each vertex is stored in the texture mapping file and eventually mapped onto the vectorized surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
켜짐 2016년 7월 27일 에서 06:51:01, Bruce Fischl (fischl@nmr.mgh.harvard.edu) 작성됨:
sure, you can do that with mri_vol2surf. Basically the initial surface and the final (inflated) surface have the same number of vertices, so the vertex identity is preserved and mri_vol2surf samples values from the volume onto the surface which can then be displayed on any surface configuration (like inflated)
On Tue, 26 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Thanks to your advice, I was able to obtain the surface of the
segmented
brain area and its inflated surface using FreeSurfer.
The generated surface however does not contain any texture, which is
needed
for further steps in my project.
I am considering to project the texture of the segmented brain area
(the
pixel intensity on the surface of the volumetric data) to the
generated
surface (vectorized surface). I wonder whether this can be done in a
similar
way to the way you project fMRI signal to the surface.
Thanks,
Younghoon Kim
Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 11:15:43 AM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
and 255 is the label that you want to cover? 16G may not be enough.
Do
you have any machines with more RAM?
On Thu, 21 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Yes Brain_FS.mgz is a segmented volume. It’s not a MRI image, and
the size is about 3000x2000x140. (We obtained this brain image using different imaging methods)
Our machine has 16GB RAM.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 21, 2016 at 10:35:18 AM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
is Brain_FS.mgz a segmented volume? How much memory do you have on
that
machine?
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
I tried "mri_tessellate Brain_FS.mgz 255 lh_test.orig.nofix”
command to generate a
surface, but received an error message as below:
changing type of input volume to 8 bits/voxel... $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 $ Cannot calloc()
Would this be because my input data is not compatible with the
mri_tessellate
command?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:29:24 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu) wrote:
If you have a segmented volume, you can use mri_tessellate to
create the
surface, then introduce the cut(s) and run mris_flatten -1 on
the
resulting
patch. You can check out our wiki
http://surfer.nmr.mgh.harvard.edu/fswiki
which has info on this process, although the flattening isn't
terribly well
documented. You need the -1 flag to tell it to only use that one
surface
that you are giving it, and not to assume that the entire FS
directory
structure exists.
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
Great! I’m not an expert in FreeSurfer, so can you give me
some
advice how
to
generate a surface of our volumetric data and flatten it?
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:12:59 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
HI Younghoon
I guess that could work. You will need to introduce at least
one
cut if not
more if you surface has substantial Gaussian curvature
cheers Bruce
On Wed, 20 Jul 2016, Younghoon Kim wrote:
Hi Bruce,
We are only interested in the surface image of the
volumetric
data.
For flattening, we do not care about the interior of the
volume, so we
would like
to remove the volume data inside.
So what we want is to peel off the surface from the
segmented
brain area
and
flatten that surface.
Thanks,
Younghoon Kim
-- Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST OMICS Lab Wellman Center, Massachusetts General Hospital Bouma’s Lab
younghoon.h.kim@gmail.com aktivhoon@kaist.ac.kr
On July 20, 2016 at 5:00:55 PM, Bruce Fischl
(fischl@nmr.mgh.harvard.edu)
wrote:
Hi Younghoon
what structure are you talking about? In general it doesn't
make sense to
flatten volumetric structures. We flatten the cortex, which
is
a folded
2D sheet. What would you do with the interior of the volume?
cheers Bruce On Wed, 20 Jul 2016, Younghoon Kim wrote:
> Hello, > > We have a volumetric data (mgz file) of a segmented brain
region. We
want
to detect > the surface of this segmented brain volume (i.e. deep
brain
region) and
flatten it > into a 2D image with its original surface texture. > > We’ve noticed that Freesurfer supports an algorithm to
flatten
volumetric
data. We > wonder if this could be adapted to our data set. Can
anyone
offer some
advice on > how to apply FreeSurfer to this more generic task? > > Thanks, > > Younghoon Kim > > -- > Younghoon Kim,Dep. of Bio and Brain Engineering, KAIST > OMICS Lab > Wellman Center, Massachusetts General Hospital > Bouma’s Lab > ---------------------------------------------- > younghoon.h.kim@gmail.com > aktivhoon@kaist.ac.kr > >_______________________________________________ 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
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The information in this e-mail is intended only for the person to
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you
in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Younghoon Kim