Unify indexing conventions and fix offset errors

[faberno]

Please describe your :rocket: feature request. SIMPAs indexing convention is messy:

• MCX starts in the middle of voxels
• kwave starts add beginning of a voxel, but we need to add +1 for matlab indexing

This behaviour and previous attempts to fix bugs introduced mulitple -1 and +1 across the code base, which are hard to understand and introduce more bugs.