1. A method for combining ultrasound image data and X-ray, MRI, or pre-implant plan image data of a material containing a plurality of markers, comprising using a computer to perform processing steps including: processing ultrasound, X-ray, or MRI image data and constructing a first volume from the image data, the first volume including data corresponding to at least a portion of the markers; processing X-ray image data, MRI image data, or pre-implant plan image data and constructing a second volume or a three dimensional (3D) point set from the image data, the second volume or 3D point set including data corresponding to at least a portion of the markers; constructing a combined image by applying 3D intensity-based registration, or a derivative thereof, to align data corresponding to the markers in the first and second volumes or the first volume and the 3D point set; and outputting the combined image comprising the ultrasound image data and the X-ray, MRI, or pre-implant plan image data of the material containing a plurality of markers.