[Freesurfer] Reading mris_smooth output using Matlab

Hi, We have segmented hippocampus using Freesurfer, and want to generate a surface which can be read into matlab. We use mri_tesselate and mris_smooth. However, the resulting file can not be read into matlab using read_surf. The error we get is ??? Undefined function or variable "vertex_coords".

[Freesurfer] mathematica and freesurfer

Hi, Does anybody have (or know of) functions for reading freesurfer's surface or curvature into Mathematica? Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] color of faces of freesurfer's surfaces

Hi, I can read (in Matlab) the freesurfer's coordinates of vertices but can not find how the colors are defined (i.e. colors of sulci versus gyri). Where can I find this information? best Nima ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] color of faces of freesurfer's surfaces

Those colors are not stored with the surfaces. Unfortunately, their definition is burried somewhere in the tksurfer code. doug [EMAIL PROTECTED] wrote: Hi, I can read (in Matlab) the freesurfer's coordinates of vertices but can not find how the colors are defined (i.e. colors of sulci versus

[Freesurfer] X11/Tkmedit/Tksurfer Issue

Hi, I'm using X11 on my Mac OS X to remotely access our Linux machine. When I try and open Tkmedit I get the following error: freeglut (/usr/local/freesurfer/stable/bin/tksurfer.bin): OpenGL GLX extension not supported by display 'localhost:10.0' I've tried using Chicken of the VNC and

Re: [Freesurfer] color of faces of freesurfer's surfaces

that's in the various curvature files (?h.curv and ?h.sulc) On Thu, 15 Nov 2007 [EMAIL PROTECTED] wrote: Hi, I can read (in Matlab) the freesurfer's coordinates of vertices but can not find how the colors are defined (i.e. colors of sulci versus gyri). Where can I find this information? best Ni

Re: [Freesurfer] mathematica and freesurfer

no sorry, although you can convert it to ascii with mris_convert On Thu, 15 Nov 2007 [EMAIL PROTECTED] wrote: Hi, Does anybody have (or know of) functions for reading freesurfer's surface or curvature into Mathematica? Nima ___ Freesurfer mailing l

Re: [Freesurfer] X11/Tkmedit/Tksurfer Issue

You must use vncserver.glx and not vncserver on the remote linux box. vncserer.glx is a special version I have setup on Martinos Linux machines. Old versions of APple X11 do not have GLX support. On Thu, 15 Nov 2007, Lauren Manning wrote: Hi, I'm using X11 on my Mac OS X to remotely access

Re: [Freesurfer] Error with mc-sess

Hi, I've tried a few more things since posting my last message but have still not been able to solve the problem with mc-sess where it hangs. I got rid of the Matlab process manager error by using Matlab 6, but the motion correction process still hangs after opening Matlab and printing >> >>INFO

[Freesurfer] loading data to matlab?

Hi, I am a newbie in using freesurfer so sorry if this is a very trivial question. I want to load my fMRI data into matlab. I want to make a matrix containing coordinates and values of all the voxels in the brain at all timepoints. I also only want the voxels that are in the gray matter a

Re: [Freesurfer] Reading mris_smooth output using Matlab

Kim, Which version of freesurfer is being used? An alternative approach is to convert the surface to ascii: mris_convert surface_file surface_file.asc where the .asc extension is an output ascii file listing the vertices and faces. Nick On Thu, 2007-11-15 at 16:18 +0100, Kim Mouridsen wrote