Re: [Freesurfer] volume of interest

On 12/17/2012 05:56 PM, octavian lie wrote:

Dear All,

I have created a volume of interest in itksnap and imported it in FS as a .mgz volume filled binary mask. How can I:

1. export it from FS in matlab and generate a .mat array containing

only the volume pixels within the volume (intensity 1) ?

You can use MRIread, like a = MRIread('youfile.mgz'); ind = find(a.vol); save('ind.mat','ind');

2. Is there a way to generate a 3D surface mesh of the boundary of the

volume of interest, as, for example, with the brain pial surface? If not, is there a way to import into FS formats such as VTK, STL or BYU meshes?

Try mri_tesselate yourfile.mgz 1 yoursurface

Thank you,

Octavian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer