Dear FreeSurfer Users,
I have a head surface mesh and a pial surface mesh obtained after segmentation of a T1 MRI scan. I am going to importing these into Homer2 Atlas Viewer as subject anatomy.
However before I can do this import successfully, I need to bring the two meshes into the same coordinate system. At the moment they are in different coordinate systems (as pictured) and I need to bring the pial surface mesh into the head surface mesh. I am a little unsure how to do this.
Does anybody have any experience with this? Or any advice on what I could do possibly?
Thanks,
Maheen
Maheen,
it sounds like a question that could be better answered by the Homer2 list.
hth d
On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui maheen.siddiqui91@gmail.com wrote:
Dear FreeSurfer Users,
I have a head surface mesh and a pial surface mesh obtained after segmentation of a T1 MRI scan. I am going to importing these into Homer2 Atlas Viewer as subject anatomy.
However before I can do this import successfully, I need to bring the two meshes into the same coordinate system. At the moment they are in different coordinate systems (as pictured) and I need to bring the pial surface mesh into the head surface mesh. I am a little unsure how to do this.
Does anybody have any experience with this? Or any advice on what I could do possibly?
Thanks,
Maheen
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,
Thanks for your reply. I have sought advice from someone who is experienced in Homer2 atlas viewer.
Is it possible to find out the the coordinate system of the T1.mgz file and the surface file created by FreeSurfer?
Thanks!
On Fri, Feb 26, 2016 at 3:36 PM, dgw dgwakeman@gmail.com wrote:
Maheen,
it sounds like a question that could be better answered by the Homer2 list.
hth d
On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui maheen.siddiqui91@gmail.com wrote:
Dear FreeSurfer Users,
I have a head surface mesh and a pial surface mesh obtained after segmentation of a T1 MRI scan. I am going to importing these into Homer2 Atlas Viewer as subject anatomy.
However before I can do this import successfully, I need to bring the two meshes into the same coordinate system. At the moment they are in
different
coordinate systems (as pictured) and I need to bring the pial surface
mesh
into the head surface mesh. I am a little unsure how to do this.
Does anybody have any experience with this? Or any advice on what I
could do
possibly?
Thanks,
Maheen
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, they are documented pretty extensively on our wiki https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On Fri, 26 Feb 2016, Maheen Siddiqui wrote:
Hi, Thanks for your reply. I have sought advice from someone who is experienced in Homer2 atlas viewer.
Is it possible to find out the the coordinate system of the T1.mgz file and the surface file created by FreeSurfer?
Thanks!
On Fri, Feb 26, 2016 at 3:36 PM, dgw dgwakeman@gmail.com wrote: Maheen,
it sounds like a question that could be better answered by the Homer2 list. hth d On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui <maheen.siddiqui91@gmail.com> wrote: > Dear FreeSurfer Users, > > I have a head surface mesh and a pial surface mesh obtained after > segmentation of a T1 MRI scan. I am going to importing these into Homer2 > Atlas Viewer as subject anatomy. > > However before I can do this import successfully, I need to bring the two > meshes into the same coordinate system. At the moment they are in different > coordinate systems (as pictured) and I need to bring the pial surface mesh > into the head surface mesh. I am a little unsure how to do this. > > Does anybody have any experience with this? Or any advice on what I could do > possibly? > > Thanks, > > Maheen >
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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks very much, I'll have a look!
On Fri, Feb 26, 2016 at 4:13 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
yes, they are documented pretty extensively on our wiki https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On Fri, 26 Feb 2016, Maheen Siddiqui wrote:
Hi,
Thanks for your reply. I have sought advice from someone who is experienced in Homer2 atlas viewer.
Is it possible to find out the the coordinate system of the T1.mgz file and the surface file created by FreeSurfer?
Thanks!
On Fri, Feb 26, 2016 at 3:36 PM, dgw dgwakeman@gmail.com wrote: Maheen,
it sounds like a question that could be better answered by the Homer2 list. hth d On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui <maheen.siddiqui91@gmail.com> wrote: > Dear FreeSurfer Users, > > I have a head surface mesh and a pial surface mesh obtained after > segmentation of a T1 MRI scan. I am going to importing these into Homer2 > Atlas Viewer as subject anatomy. > > However before I can do this import successfully, I need to bring the two > meshes into the same coordinate system. At the moment they are in different > coordinate systems (as pictured) and I need to bring the pial surface mesh > into the head surface mesh. I am a little unsure how to do this. > > Does anybody have any experience with this? Or any advice on what I could do > possibly? > > Thanks, > > Maheen >
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 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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
dgw -
Maheen Siddiqui