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