Hi Tara,

>
> First, how would it be best to get this into a
> normalized space (i.e. MNI). Should I map it using
> the MNI spec files to the MNI volume, or could I
> 3dSurf2Vol it on a subject then warp the mask to
> MNI space.

Go with the first option, which would be trivial if you are using standard meshes. Load the dataset onto the MNI surfaces of matching topology (same mesh) and then map the regions to the volume.
>
> Additionally, I grabbed the 2nd example for
> 3dSurf2Vol and I have a couple of questions about
> that. Where does the 10.1d file come from, and is
> the 0.6 a threshold for inclusion of a voxel?

sdata_10.1D is a 1D file containing a value for each node you want to map into the volume
In your case, you probably have a dataset in .niml or .gii format, though any format is OK.
The cmask option below is meant to restrict which voxels in the grid_parent should be processed. In the example, the mask is generated on the fly for those voxels in fred_func+orig, sub-brick 2, which exceed a value of 0.6 .

cheers
z

>
> 3dSurf2Vol \
> -spec fred.spec
> \
> -surf_A smoothwm
> \
> -surf_B pial
> \
> -sv fred_anat+orig
> \
> -grid_parent 'fred_func+orig[0]'
> \
> -cmask '-a fred_func+orig[2] -expr
> step(a-0.6)' \
> -sdata_1D sdata_10.1D
> \
> -map_func ave
> \
> -f_steps 15
> \
> -f_index points
> \
> -prefix fred_surf_ave
>
> Thanks for the help!
>
> Tara