Thanks Greg - I think you pretty much covered the possible sources of errors :)

Just to add a bit of theoretical background why often one would want the inverse transformation:

Say you align image A to image B via transform X such that you can reslice B to match A.

Then if your neuron model is in the coordinates of image B, in order to get it transformed into the space of A, you need to apply the inverse of X.

That is because for reslicing, one takes the coordinate of each pixel in A, maps it to B via X, then pulls back the interpolated image intensity from B. So intensities move the opposite direction between coordinate systems as do geometries (e.g., pixel or model coordinates).

Best,
  Torsten