Please upload an archive file with a sample scene with fiducials and a volume, and give me a note about what output you expect.
Oh, and if you can give me a slicer2 scene that works, that would help a lot.

Need to check if need to invert the matrix.

let me know if the scene does not open or if it is missing anything that you need. thanks!

doug

I don't have permission to read /projects/schiz/3Tdata, could you copy the files that this scene file references into a directory in /spl/tmp for me?

all the files are now in /spl/tmp/dougt/realign_test with group 'schiz' permissions... that should be okay. scene has been resaved. let me know if there are problems.

Nicole will remove the resampling option and documentation will suggest using the Resample Scalar Volume module to apply the transform.

For testing, use the two attached .fcsv files, output transform should be manual0 from the attached scene file:
0.991835 0.127383 -0.00605555 0
-0.124577 0.957649 -0.259595 0
-0.0272689 0.25823 0.965699 0
0 0 0 1

Code checked in, need to add a nightly test.