Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in the file? I am trying to find all the neighborhood of any given vertex as x,y,z -> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in the file? I am trying to find all the neighborhood of any given vertex as x,y,z -> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations and a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
________________________________ Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex
Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in the file? I am trying to find all the neighborhood of any given vertex as x,y,z -> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations and a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
________________________________ Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex
that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations and a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations
and
a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Hi Bruce;
Unfortunately still we have the same problem.
I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52
I also executed "recon-all -make all" script as you suggested but nothing changed.
When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double
Any ideas?
________________________________ Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex
nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations
and
a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Thickness isn't a surface, it's a scalar field. Use read_curv for it
On Dec 23, 2016, at 11:09 AM, Onur Uğurlu T_mac_ONUR@hotmail.com wrote:
Hi Bruce;
Unfortunately still we have the same problem.
I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52
I also executed "recon-all -make all" script as you suggested but nothing changed.
When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double
Any ideas?
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex
nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations
and
a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce;
It works! I didn't know that it's a scalar.
Thanks for the help.
sincerely yours,
Onur
________________________________ Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 23 Aralık 2016 Cuma 22:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Ynt: Neighborhood of a vertex
Thickness isn't a surface, it's a scalar field. Use read_curv for it
On Dec 23, 2016, at 11:09 AM, Onur Uğurlu <T_mac_ONUR@hotmail.commailto:T_mac_ONUR@hotmail.com> wrote:
Hi Bruce;
Unfortunately still we have the same problem.
I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52
I also executed "recon-all -make all" script as you suggested but nothing changed.
When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double
Any ideas?
________________________________ Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex
nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations
and
a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Bruce,
Now I can get thickness values, vertex locations and the faces. But it seems every subject has a different number of vertices. In my case Subject1 has 107107 vertices, whereas Subject2 has 133093. Is it possible to normalized the subjects into same space?
Thanks for the all help. sincerely yours,
Onur
________________________________ Gönderen: Onur Uğurlu T_mac_ONUR@hotmail.com adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 25 Aralık 2016 Pazar 23:56 Kime: Freesurfer support list Konu: [Freesurfer] Ynt: Ynt: Ynt: Ynt: Neighborhood of a vertex
Hi Bruce;
It works! I didn't know that it's a scalar.
Thanks for the help.
sincerely yours,
Onur
________________________________ Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 23 Aralık 2016 Cuma 22:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Ynt: Neighborhood of a vertex
Thickness isn't a surface, it's a scalar field. Use read_curv for it
On Dec 23, 2016, at 11:09 AM, Onur Uğurlu <T_mac_ONUR@hotmail.commailto:T_mac_ONUR@hotmail.com> wrote:
Hi Bruce;
Unfortunately still we have the same problem.
I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52
I also executed "recon-all -make all" script as you suggested but nothing changed.
When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double
Any ideas?
________________________________ Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex
nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running recon-all script with -qcache option, and trying to match this data with lh.thickness file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on your input surface. Can you load the thickness as a surface overlay? It may be that you regenerated surface and not the htickness, or visa-versa. Which surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex locations
and
a list of faces. However, the list contains 107106 vertices whereas the lh.thickness.asc file contains 118603 vertices. How can I match the thickness values which are inlh.thickness.asc file with the vertices which were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
Gönderen: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> adına freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can load a surface file in with read_surf.m. The <vertex index> will then be an index into the surface (although note that you will need to add 1 to it since matlab is 1-based when you index into the vertex list). It will return a list of vertex locations and also a list of faces. The faces contain the (0-based) indices of the vertices in each triangle, which can be used to compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values of each vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z values in
the
file? I am trying to find all the neighborhood of any given vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, you can use mri_surf2surf to map the thicknesses to fsaverage space (this is what recon-all -qcache does)
cheers Bruce
On Tue, 24 Jan 2017, Onur Uğurlu wrote:
Dear Bruce,
Now I can get thickness values, vertex locations and the faces. But it seems every subject has a different number of vertices. In my case Subject1 has 107107 vertices, whereas Subject2 has 133093. Is it possible to normalized the subjects into same space?
Thanks for the all help.
sincerely yours,
Onur
Gönderen: Onur Uğurlu T_mac_ONUR@hotmail.com adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 25 Aralık 2016 Pazar 23:56 Kime: Freesurfer support list Konu: [Freesurfer] Ynt: Ynt: Ynt: Ynt: Neighborhood of a vertex
Hi Bruce;
It works! I didn't know that it's a scalar.
Thanks for the help.
sincerely yours,
Onur
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 23 Aralık 2016 Cuma 22:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Ynt: Neighborhood of a vertex Thickness isn't a surface, it's a scalar field. Use read_curv for it
On Dec 23, 2016, at 11:09 AM, Onur Uğurlu T_mac_ONUR@hotmail.com wrote:
Hi Bruce;Unfortunately still we have the same problem.
I've executed "recon-all -all -s SubjID" script, and here are the time stamps for these 2 files lh.orig => 01:56:56 lh.thickness => 04:07:52
I also executed "recon-all -make all" script as you suggested but nothing changed.
When i use "read_surf" function in Matlab on "lh.thickness" and the answer is 489x3 double When i use "[coords, faces]=read_surf" function on "lh.orig" , "corrds" is 125312x3 double and the "faces" is 250620x3 double
Any ideas?
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 21 Aralık 2016 Çarşamba 00:05 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Ynt: Neighborhood of a vertex nope, that should be fine, but the lh.thickness should have exactly as many entries as the lh.orig. If not, it means one was regenerated and the other wasn't. What are the dates on the two files? The lh.thickness should be newer than the lh.orig. If it isn't, you probably edited and reran part of recon-all but not all the way through. You could also try recon-all -make all and it will rerun things if it thinks they are needed
On Tue, 20 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
I am using lh.orig file located in "surf" directory after running
recon-all
script with -qcache option, and trying to match this data with
lh.thickness
file again in the same directory. Am I using a wrong combination ?
sincerely yours,
Onur
_
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 19 Aralık 2016 Pazartesi 19:48 Kime: Freesurfer support list Konu: Re: [Freesurfer] Ynt: Neighborhood of a vertex that shouldn't be the case. Run mris_info or mris_euler_number on
your
input surface. Can you load the thickness as a surface overlay? It
may be
that you regenerated surface and not the htickness, or visa-versa.
Which
surface are you using?
On Mon, 19 Dec 2016, Onur Uğurlu wrote:
Hi Bruce,
Thank you so much for the answer.
I have used "read_surf.m" function and got the list of vertex
locations
and
a list of faces. However, the list contains 107106 vertices
whereas the
lh.thickness.asc file contains 118603 vertices. How can I match
the
thickness values which are inlh.thickness.asc file with the
vertices which
were obtained from "read_surf.m" function?
Sincerely yours,
Onur
_
_
Gönderen: Bruce Fischl fischl@nmr.mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 18 Aralık 2016 Pazar 17:54 Kime: Freesurfer support list Konu: Re: [Freesurfer] Neighborhood of a vertex Hi Onur
for that you need a surface file. If you are using matlab you can
load a
surface file in with read_surf.m. The <vertex index> will then be
an index
into the surface (although note that you will need to add 1 to it
since
matlab is 1-based when you index into the vertex list). It will
return a
list of vertex locations and also a list of faces. The faces
contain the
(0-based) indices of the vertices in each triangle, which can be
used to
compile a list of neighbors.
cheers Bruce
On Sun, 18 Dec 2016, Onur Uğurlu wrote:
Hi all,
I have a 'lh.thickness.asc' file which contains thickness values
of each
vertex.
The format of the file is following;
<vertex index> <x> <y> <z> <thickness>
However, x,y,z are not integer. What is the unit of the x,y,z
values in
the
file? I am trying to find all the neighborhood of any given
vertex as
x,y,z
-> x+1,y,z etc, can you suggest a method for this problem.
Sincerely yours,
Onur
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Onur Uğurlu