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Currently, the initial alignment between the data and template are done manually by adjusting the yaw/pitch/roll of the atlas to transform the template such that it aligns with the data. In order for the outputs to match brainreg, the three letter brainglobe-space notation needs to be stored in the metadata. If we're taking this as a user input, the workflow should instead use brainglobe-space to transform the data to roughly align with the template.