There's a how-to in the FreeSurfer website:
http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo

Pedro Paulo Jr.

On Mon, Feb 20, 2012 at 23:32, Manfred G Kitzbichler <
manfr...@nmr.mgh.harvard.edu> wrote:

>  Hi Darshan,
>
> as Bruce suggested, you can use mris_convert to get an STL file which you
> can import into Blender or MeshLab. Both write Wavefront OBJ files.
>
>     - Manfred
>
>
>
> On 02/20/2012 07:24 PM, Darshan P wrote:
>
>  Hello all,
>
>  I was wondering if I can convert the surface outputs to an OBJ mesh file
> format .
> Since most of the applications are in windows I was hoping if there is
> conversion tool to do this .
>
>  Regards
> Darshan
>
>
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>
>
> --
> Manfred G. 
> Kitzbichler<https://www.nmr.mgh.harvard.edu/martinos/people/showPerson.php?people_id=1377>,
> Research Fellow
> Harvard Medical School & Mass General Hospital
> Martinos Center for Biomedical Imaging
> 149 Thirteenth Street, Rm 10.018
> Charlestown, MA 02129, USA
>
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