hi Gonzalo –
The obj format used in BrainSuite is the MNI obj format, which was more widely used when we first developed BrainSuite.
There is a way to get a Wavefront obj file from BrainSuite — if you save out a surface file using .wfo as the extension (I used wfo to represent WaveFront Obj) and then change the extension to .obj, you should be able to use it in programs that read Wavefront Obj files. I do this sometimes when I want to look at BrainSuite surfaces in Meshlab, and it works fine.
You can also use a .stl extension, and the surface will be saved in STL format. Some of our users have used this to 3D print brain models made in BrainSuite.
Just one note — both of these formats lose some of the information that BrainSuite uses in its different functions.
Give it a try and let us know if it works for you.