Hi Ziad,

You helped me greatly with this at the 2014 bootcamp, and I was able to use the mask for surface based analyses. Now I am trying to convert the mask to the volume and I have a few questions about this.

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.

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?

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