If you leave the -prefix off, then to3d will open the GUI. Other inconsistencies or lack of information can also trigger the GUI. On the commandline, the thickness is determined by the xFOV,yFOV,zFOV or xSLAB,ySLAB,zSLAB options for to3d. You can also change slice thickness in the header with "3drefit -zdel n.nn -keepcen".