1. a difference in the convention for row-major and column-major representation of the matrix. Essentially you may need to transpose.
2. a difference in your expectations about the transformation direction. You may actually want the inverse of what you have tried to apply.

Thanks, Greg.  I had previously been trying to transpose the matrix, but it ended up being the latter case of needing the inverse of the transformation matrix.

And I'm specifically happy to get advice from you, as now that I have a set of registered, traced neurons, I would like to compare them to each other using NBLAST.

I imagine this is a conversation we could/should have elsewhere, but I'd love some advice on how to run NBLAST on pairs of my own (non-fly) neurons.  Is there a best manner to contact you for such a query?

Cheers,

Zane