Dear Ying,
by default, Coregister Estimate applies the reorientation to supplied "Source" and "Other" images. The reorientation matrix used is not saved by default, but it is available as an optional dependency in the batch system. The attached batch shows how to save this matrix into a file for future reference. You can use this saved matrix later to run "Tools->Reorient Images" on other images which were not coregistered during Coregister Estimate.
Hope this helps,
Volkmar
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