As currently written, the Stitch Volumes module only works for stitching together image volumes which are distributed along one axis (like a series of CT or MR volumes taken at different table position stations). Trying to combine overlapping MR imaging with higher resolution in differing orientations is a very different problem and would require a different approach. This is a common desire because this is often how clinical imaging is collected, but there is not a commonly-used, effective way to generate a high resolution volume from multiple anisotropic image volumes (at least not that I am aware of).
Here are some links to other discussions where someone wanted to do this where you can find some explanations and suggestions: