Dear FreeSurfer,
Hi,
I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer.
I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html)
I converted ?h.sphere.reg file into ?h.sphere.reg.asc using *mris_convert* command, and imported it to MATLAB using *read_asc.m* file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information.
I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates.
Thank you, Jihoon Oh
Hi Jihoon,
You can just use read_surf.m, e.g.
[vertices, faces] = read_surf('lh.sphere.reg');
The vertices is a N x 3 matrix. Row 1 corresponds to vertex 1, etc.
--Thomas
On Wed, Mar 14, 2012 at 12:23 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Dear FreeSurfer,
Hi,
I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer.
I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html)
I converted ?h.sphere.reg file into ?h.sphere.reg.asc using mris_convert command, and imported it to MATLAB using read_asc.m file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information.
I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates.
Thank you, Jihoon Oh
--
Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon@gmail.com
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.
Thank you for your response. Although I followed your instructions, in my system, it seems that two coordinates are not the same.
When I read sphere.reg through the function [vertices, faces] = read_surf('rh.sphere.reg'), the first row reads [-21.02, -94.94, -23.32]. but when I use tksurfer and click the vertex #1, spherical X,Y,Z represents [27.92, -93.92, -15.44].
When I reconstruct surface (blue colored label in the attached screenshot1) using the row number as the vertex index in MATLAB, two separate surfaces are presented in 3D space (screenshot2), not simliar to original one.
I attached related screenshots and .mat file of my results.
Thanks for your help again.
with Regards, Jihoon Oh
On Wed, Mar 14, 2012 at 3:16 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Jihoon,
You can just use read_surf.m, e.g.
[vertices, faces] = read_surf('lh.sphere.reg');
The vertices is a N x 3 matrix. Row 1 corresponds to vertex 1, etc.
--Thomas
On Wed, Mar 14, 2012 at 12:23 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Dear FreeSurfer,
Hi,
I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer.
I found following archives that are related to this question, but I
couldn't
find any vertex index (number) information in a sphere.reg file. (
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html)
I converted ?h.sphere.reg file into ?h.sphere.reg.asc using mris_convert command, and imported it to MATLAB
using read_asc.m file
(without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information.
I wonder if there is a way to read the vertex index from a sphere.reg
file,
or there are other methods that read both vertex index and spherical coordinates.
Thank you, Jihoon Oh
--
Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon@gmail.com
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.
Sorry. I meant row 1 should be vertex 0, row 2 should be vertex 1, etc...
--Thomas
On Wed, Mar 14, 2012 at 3:59 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Thank you for your response. Although I followed your instructions, in my system, it seems that two coordinates are not the same.
When I read sphere.reg through the function [vertices, faces] = read_surf('rh.sphere.reg'), the first row reads [-21.02, -94.94, -23.32]. but when I use tksurfer and click the vertex #1, spherical X,Y,Z represents [27.92, -93.92, -15.44].
When I reconstruct surface (blue colored label in the attached screenshot1) using the row number as the vertex index in MATLAB, two separate surfaces are presented in 3D space (screenshot2), not simliar to original one.
I attached related screenshots and .mat file of my results.
Thanks for your help again.
with Regards, Jihoon Oh
On Wed, Mar 14, 2012 at 3:16 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Hi Jihoon,
You can just use read_surf.m, e.g.
[vertices, faces] = read_surf('lh.sphere.reg');
The vertices is a N x 3 matrix. Row 1 corresponds to vertex 1, etc.
--Thomas
On Wed, Mar 14, 2012 at 12:23 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Dear FreeSurfer,
Hi,
I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer.
I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file.
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html)
I converted ?h.sphere.reg file into ?h.sphere.reg.asc using mris_convert command, and imported it to MATLAB using read_asc.m file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information.
I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates.
Thank you, Jihoon Oh
--
Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon@gmail.com
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.
--
Jihoon Oh, M.D. Public Health Doctor
Sanyang public health subcenter Gyeongsangbuk-do, 745-822, South Korea +82-10-2712-2212 (Mobile) E-mail: ojihoon@gmail.com
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.
Dear Thomas,
Thanks for your help! It works out well.
Jihoon Oh
On Wed, Mar 14, 2012 at 5:32 PM, Thomas Yeo ythomas@csail.mit.edu wrote:
Sorry. I meant row 1 should be vertex 0, row 2 should be vertex 1, etc...
--Thomas
On Wed, Mar 14, 2012 at 3:59 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Thank you for your response. Although I followed your instructions, in my system, it seems that two coordinates are not the same.
When I read sphere.reg through the function [vertices, faces] = read_surf('rh.sphere.reg'), the first row reads [-21.02, -94.94, -23.32]. but when I use tksurfer and click the vertex #1, spherical X,Y,Z represents [27.92, -93.92, -15.44].
When I reconstruct surface (blue colored label in the attached screenshot1) using the row number as the vertex index in MATLAB, two separate surfaces are presented in 3D space (screenshot2), not
simliar
to original one.
I attached related screenshots and .mat file of my results.
Thanks for your help again.
with Regards, Jihoon Oh
On Wed, Mar 14, 2012 at 3:16 PM, Thomas Yeo ythomas@csail.mit.edu
wrote:
Hi Jihoon,
You can just use read_surf.m, e.g.
[vertices, faces] = read_surf('lh.sphere.reg');
The vertices is a N x 3 matrix. Row 1 corresponds to vertex 1, etc.
--Thomas
On Wed, Mar 14, 2012 at 12:23 PM, Ji hoon Oh ojihoon@gmail.com wrote:
Dear FreeSurfer,
Hi,
I have a label with vertex index, RAS and overlay values, and want to add spherical coordinates to them as presented in tksurfer.
I found following archives that are related to this question, but I couldn't find any vertex index (number) information in a sphere.reg file.
(
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00627.html)
I converted ?h.sphere.reg file into ?h.sphere.reg.asc using mris_convert command, and imported it to MATLAB using read_asc.m file (without face data). They had [x,y,z] coordinates in columns, but did not provide vertex index information.
I wonder if there is a way to read the vertex index from a sphere.reg file, or there are other methods that read both vertex index and spherical coordinates.
Thank you, Jihoon Oh
--
Jihoon Oh, M.D. Ph.D. candidate, Bio and Brain Engineering Korea Advanced Institute for Science and Technology (KAIST) E-mail: ojihoon@gmail.com
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.
--
Jihoon Oh, M.D. Public Health Doctor
Sanyang public health subcenter Gyeongsangbuk-do, 745-822, South Korea +82-10-2712-2212 (Mobile) E-mail: ojihoon@gmail.com
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
-
Ji hoon Oh -
Thomas Yeo