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Thank you for the suggestions.

I have followed your pipeline of pre-alignment and used the Wiki parameters to try and adjust my output to no avail. Here is a list of the parameters I have already tried changing.

Initial Alignment changed from Current Pose to Volume Center
Tried both Anisotropic Scale and Affine Transform

Changed Grid Spacing from 80 to 120

Decreased and increased energy weight
Set Jacobian Weight to 0.1

Set Inverse Consistency Weight to 0.1

Turned on final full-resolution warp optimization.

Are there any other parameters or pipeline changes I can make to achieve alignment that actual expands the top and bottom of my sample brains to fit the reference one?

Thank You