The foot consists of many small bones with complicated joints that guide and limit motion. A variety of invasive and noninvasive means [mechanical, X-ray stereophotogrammetry, electromagnetic sensors, retro-reflective motion analysis, computer tomography (CT), and magnetic resonance imaging (MRI)] have been used to quantify foot bone motion. In the current study we used a foot plate with an electromagnetic sensor to determine an individual subject’s foot end range of motion (ROM) from maximum plantar flexion, internal rotation, and inversion to maximum plantar flexion, inversion, and internal rotation to maximum dorsiflexion, eversion, and external rotation. We then used a custom built MRI-compatible device to hold each subject’s foot during scanning in eight unique positions determined from the end ROM data. The scan data were processed using software that allowed the bones to be segmented with the foot in the neutral position and the bones in the other seven positions to be registered to their base positions with minimal user intervention. Bone to bone motion was quantified using finite helical axes (FHA). FHA for the talocrural, talocalcaneal, and talonavicular joints compared well to published studies, which used a variety of technologies and input motions. This study describes a method for quantifying foot bone motion from maximum plantar flexion, inversion, and internal rotation to maximum dorsiflexion, eversion, and external rotation with relatively little user processing time.