Hi Lisa,

Glad that to hear that the scripts have been working out for you!

Yes, the wm and csf mask can be quite limited. We deliberately set a pretty high treshold to avoid inclusion of any other signal in the mask. (this might be important if one would wish not to do global correction). We included the overlap with priors to make sure that the tissue that is selected is generally (i.e., in the template) regarded as csf or wm. That way we try to avoid possible errors due to non-optimal segmentation or registration.

We've also been using this procedure successfully with kids before. The priors are indeed for adults, but then again most people are using an adult atlas for children (although this is a much debated issue).

To see the overlap you have to adjust the header of the .nii file to tailarach view. This is best done by 3dcopy the file (e.g., "3dcopy test.nii.gz test2"), this will recreate your file in AFNI format. Afterwards you can adjust the view with "3drefit -view tlrc test2"
Alternatively, you should be able to overlay the two images in fslview.

Hope this helps!
Also, keep an eye on the site as we will be releasing some developmental data (including kids) in the near future.
Maarten