Hi Shani, it looks like your commands are right. How are you judging that the mask is thicker? What is the resolution of the DTI volume? When you binarize in a coarser space, you'll naturally not get it to line up with the surface, and the binary mask will naturally be thicker. doug

On 02/21/2013 08:22 AM, Shani Ben Amitay wrote:

Dear freesurfers

I'm using bbregister and mri_surf2surf to transform intermediate cortical surfaces and mid surfaces normals to diffusion space. Next I'm trying to generate volumes from these surfaces (in the same diffusion space), however the generated volumes are much thicker then the generated surfaces. for example to generate surface normals I used the following: mri_surf2surf --s subjectid --hemi lh --sval-nxyz white_surface_in_diffusion --tval lhwhitediffusion_n.mgh mri_surf2vol --surfval lhwhitediffusion_n.mgh --hemi lh --surf white --reg mri/register.dat --outvol lh_white_n.img --template lowb.img Any idea what am I doing wrong?

Thanks!

Shani

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