All ScanImage analog inputs are configured as 'differential' inputs by default (except where stated differently). On National Instruments DAQ boards two analog input terminals are required for this terminal configuration. An differential analog input task for AI0 returns the potential between AI0 and AI8.
On BNC-based breakout boxes from National Instruments, the BNC core is connected to AIx, the BNC shield to AIx+8, so that no further action is required (On BNC-2090x ensure the SE/DIFF slider for the input terminals are set to 'DIFF'). However, on NI breakout boxes with screw terminals (SCB-68(A) or USB DAQ devices) this connection needs to be made manually. To measure AI0, connect the positive wire to AI0, the negative wire to AI8. To measure AI1, connect the positive wire to AI1, the negative wire to AI9 and so on.
To learn more about the different analog input terminal configurations available on National Instruments DAQ boards review the NI knowledgebase Grounding Considerations for Improved Measurements.