Hi Adam,
if you have your other images available when you run "Coregister: Estimate&Reslice", you can add them as "Other images". Since you seem to plan to reslice your images to a reference image with a different resolution than the Coregister-reference, you could just run "Coregister: Estimate" and do the reslicing separately.
If you need to reorient images which are not available when running "Coregister: Estimate&Reslice", you can save the transformation matrix with "Basic IO->Variable Input/Output->Save Variables". "Coregister: Estimate(&Reslice)" will provide the transformation matrix as a dependency for "Variable contents" of the "Save Variables" module. You can then load this variable using "Basic IO->Variable Input/Output->Load Variables from .mat file" and use it for reorientation.
Hope this helps
Volkmar
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