afni.nimh.nih.gov

You need to read the to3d manual carefully. How to set the slice offsets correctly is explained in there in detail, and I don't want to repeat that. Also, to3d can now read the header info from various scanner formats (GE, Siemens, and DICOM) and can use that to set the geometrical information automatically. So the program may do the work for you, if you have image files in a format that to3d understands well.

bob cox