Hi Eric,

Just a clarification about my suggestion regarding masking.
What I was proposing was to mask the IIT HARDI template by creating a more brain-specific mask. To make that mask you can:
1) mask the WM probability map we provide using a threshold of ~0.5,
2) mask the GM probability map we provide using a threshold of ~0.5,
3) combine the two masks (OR).

You can then apply the mask to the IIT HARDI template (which will better restrict the template to brain tissue) and redo the registrations.

Regards,
Konstantinos