External Email - Use Caution
Hi
I am using freesurfer to extract just the cortical surface mesh. Next, I want to map each vertex on the surface mesh to its corresponding voxel in the volumetric atlas. Any help how to go forward with it?
Regards Raunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
Hi Raunak
this page should have the info you need:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
cheers Bruce On Thu, 6 Jun 2019, Raunak Swarnkar wrote:
External Email - Use Caution
Hi I am using freesurfer to extract just the cortical surface mesh. Next, I want to map each vertex on the surface mesh to its corresponding voxel in the volumetric atlas. Any help how to go forward with it?
RegardsRaunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
External Email - Use Caution
Dear Dr. Fischl
Thank you for your reply. I was going through the same reference earlier. However, as per my understanding, this page talks about converting a single point on cortical surface to another space. What I want to achieve is to extract all the vertices from the cortical surface in some form of displacement vector field, where I have the 3 dimensional co-ordinates for all the vertices in a matrix. Once I have this matrix, I can then convert it into MNI or any other space as mentioned in the page. However, I am not clear on how to extract all of these vertices from the cortical surface in some sort of matrix. Can you recommend some way to achieve this?
Regards Raunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
On Thu, Jun 6, 2019 at 1:40 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Raunak
this page should have the info you need:
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
cheers Bruce On Thu, 6 Jun 2019, Raunak Swarnkar wrote:
External Email - Use CautionHi I am using freesurfer to extract just the cortical surface mesh. Next, I
want to map each vertex on
the surface mesh to its corresponding voxel in the volumetric atlas. Any
help how to go forward with
it?
RegardsRaunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Raunak
you can either load the surface into matlab using read_surf.m or convert to asci via:
mris_convert lh.white lh.white.asc
cheers Bruce On Mon, 10 Jun 2019, Raunak Swarnkar wrote:
External Email - Use Caution
Dear Dr. Fischl Thank you for your reply. I was going through the same reference earlier. However, as per my understanding, this page talks about converting a single point on cortical surface to another space. What I want to achieve is to extract all the vertices from the cortical surface in some form of displacement vector field, where I have the 3 dimensional co-ordinates for all the vertices in a matrix. Once I have this matrix, I can then convert it into MNI or any other space as mentioned in the page. However, I am not clear on how to extract all of these vertices from the cortical surface in some sort of matrix. Can you recommend some way to achieve this?
RegardsRaunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
On Thu, Jun 6, 2019 at 1:40 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Raunak
this page should have the info you need: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems cheers Bruce On Thu, 6 Jun 2019, Raunak Swarnkar wrote: > > External Email - Use Caution > > Hi > I am using freesurfer to extract just the cortical surface mesh. Next, I want to map each vertex on > the surface mesh to its corresponding voxel in the volumetric atlas. Any help how to go forward with > it? > > RegardsRaunak Swarnkar > Visiting Student Researcher - Summer 2019 > Dept. of Mathematics & Statisitcs, uOttawa > MSc Cognitive Science Student, IIT Gandhinagar > >_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Dr. Fischl
Got it. Thank you very much.
Regards Raunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
On Mon, Jun 10, 2019 at 3:31 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Raunak
you can either load the surface into matlab using read_surf.m or convert to asci via:
mris_convert lh.white lh.white.asc
cheers Bruce On Mon, 10 Jun 2019, Raunak Swarnkar wrote:
External Email - Use CautionDear Dr. Fischl Thank you for your reply. I was going through the same reference
earlier. However, as per my
understanding, this page talks about converting a single point on
cortical surface to another space.
What I want to achieve is to extract all the vertices from the cortical
surface in some form of
displacement vector field, where I have the 3 dimensional co-ordinates
for all the vertices in a
matrix. Once I have this matrix, I can then convert it into MNI or any
other space as mentioned in
the page. However, I am not clear on how to extract all of these
vertices from the cortical surface
in some sort of matrix. Can you recommend some way to achieve this?
RegardsRaunak Swarnkar Visiting Student Researcher - Summer 2019 Dept. of Mathematics & Statisitcs, uOttawa MSc Cognitive Science Student, IIT Gandhinagar
On Thu, Jun 6, 2019 at 1:40 PM Bruce Fischl fischl@nmr.mgh.harvard.edu
wrote:
Hi Raunak this page should have the info you need: https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems cheers Bruce On Thu, 6 Jun 2019, Raunak Swarnkar wrote: > > External Email - Use Caution > > Hi > I am using freesurfer to extract just the cortical surface mesh.Next, I want to map
each vertex on > the surface mesh to its corresponding voxel in the volumetricatlas. Any help how to
go forward with > it? > > RegardsRaunak Swarnkar > Visiting Student Researcher - Summer 2019 > Dept. of Mathematics & Statisitcs, uOttawa > MSc Cognitive Science Student, IIT Gandhinagar > >_______________________________________________ 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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Raunak Swarnkar