Re: [Freesurfer] can not see surfaces

2007-03-01 Thread Burak Ozkalayci
(goto the nvidia site to do this). This problem, of displaying a sliver in tksurfer, has been seen before, and upgrading the driver will fix it. Nick On Thu, 2007-03-01 at 17:10 +0100, Burak Ozkalayci wrote: Hi all, I am new to freesurfer. I just installed the freesurfer 3.0.5 to my computer

[Freesurfer] volume index vertex positions

2007-04-13 Thread burak ozkalayci
Hi surfers, Last time I asked how to see and access to the thickness values and your advices worked. Thanks a lot. When I checked the asci file, which I acquired by converting the thickness file, I saw that the X Y Z coordinates of the vertices are given in talairach coordinates. However I ne

[Freesurfer] Grainy thickness ribbon

2007-04-18 Thread burak ozkalayci
Dear surfers, I try to get a thickness map of the cortex by using the mri_surf2vol function. However when I used it like : mri_surf2vol --volreg reg.dat --surfval ../surf/lh.thickness_max --hemi lh --template ./orig/001.mgz --outvol leftThickness_max_filled_pial.nii --fillribbon it genera

[Freesurfer] vertex normals

2007-05-04 Thread burak ozkalayci
Hi all, I want to get an ascii file listing the normal vectors of each vertex of the surface (white or pial). In http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02210.html mri_surf2surf is adviced to used but I could not find any example usage for creating vertex normals. And I

Re: [Freesurfer] vertex normals

2007-05-08 Thread Burak Ozkalayci
On Fri, 2007-05-04 at 18:46 +0200, burak ozkalayci wrote: Hi all, I want to get an ascii file listing the normal vectors of each vertex of the surface (white or pial). In http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02210.html mri_surf2surf is adviced to used but I could n

[Freesurfer] About tissue probability maps from aseg.mgz

2007-10-22 Thread Burak Ozkalayci
Dear surfers, I want to ask whether it is possible to have a tissue probability map of the brain according to aseg.mgz. If I am not wrong aseg.mgz is the MAP estimate of a Markov Random Field based segmentation hence we shall get the probability maps for each label or tissue. Is it possible?