Dear Lily,
the idea is to keep the resolution of your functional data. In human fMRI, (roughly) isotropic voxels of ~ 3 x 3 x 3 mm are common, and during normalisation step the resolution is typically increased to 2 x 2 x 2.
If the resolution is 0.5 x 0.5 mm in plane in case of your mice, go with it. If it's 0.25 x 0.25 mm, use these values. Probably it doesn't make much sense to increase the resolution any further during the normalisation step because the original resolution is already poorer along the z axis (slice thickness).
Best,
Helmut
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