to3d only uses information from the files, as far as I remember.
Generally, the default is to copy exactly the values in the input
data files. There are also options you can set, for example, if
you're using DICOM files, you can use the DICOM windowing
to rescale values.
I can't think of anything in to3d that would change relative
values within a single dataset. What format are you
converting from? Have you looked at the original data?
rich