feat: refactor MRIScan to reflect BIDS standards

[dbirman]

This PR updates MRIScan to better reflect the BIDS standards for MRI. The included changes would normally be breaking, but MRIScan has not been used yet in the metadata.

• MRIScan.scan_index -> index, better description
• MRIScan.setup added, True for positioning/shim sequences, false for data sequences that will be used for analysis
• MRIScan.primary_scan removed
• MRIScan.scan_type -> mr_acquisition_type, restricted to "2D/3D" to match BIDS standard
• MRIScan.scan_sequence_type -> pulse_sequence_type, to match BIDS standard
• MRIScan.scan_coordinate_system -> scanner_coordinate_system
• MRIScan.scan_affine_transform -> affine_transform
• _unit fields default to S to match BIDS standard
• Example updated
• Docs updated