hi @mkn,
I am not sure the indexing will work correctly following your import+renaming workflow. The reason (and that will answer your first question too) is that the indexing is done directly on the 'Output.h5' files and completely ignores the .smash ones. So renaming the simulations in the Sim4Life project may not have the desired effect, unless it also modifies the Output.h5 results.
The indexing also does not move, modify or otherwise reorganize your collection of Output.h5 files. This has to be done manually, following the folder hierarchy that I described earlier. The indexing itself simply parses the files it finds and builds an index (ending with .sqlite). It is basically at this stage that your output.h5 files acquire some semantic "meaning" (i.e. that they are associated with a given birdcage coil, anatomical model, etc...).
The "position" is indeed the relative position of the body with respect to the coil. In MRIxViP, the landmark position is defined as the distance between the isocenter of a given bone in the skull of the body and the isocenter of the coil, along the direction of the z-axis of the coil. Note that IMAnalytics will blindly trust that the Output.h5 files it finds in a given folder correspond to the configuration determined by the indexing process (i.e. the labelling of the data is done by placing the files in the correct folders).
