Following spinal cord injury (SCI), morphological changes in the spinal cord are observed at the clinically diagnosed level of injury, as well as at segmental levels above and below the injury site due to axonal degeneration. In order to quantify the extent of morphological changes, a three dimensional segmentation of the spinal cord was constructed using magnetic resonance images (MRI) of the cervical spinal cord. Six neurologically intact (NI) and five spinal cord injured (SCI) subjects were scanned using an axial, T2 weighted fluid-attenuated inversion recovery (FLAIR) sequence. The boundaries of the spinal cord volume were then identified using a three-dimensional, seeded region growing technique. The area of 4 slices approximating the C3 segment were measured and the mean area was calculated for each subject. In NI subjects the mean C3 cord area was 75.2 +/- 11 mm(2). In contrast, SC subjects had a mean C3 cord area of 60.4 +/- 7.3 mm(2). This 20% decrease in area for the SCI subjects, compared to the NI subjects, was statistically significant (t-test, p<0.05). These results show that the narrowing of the spinal cord after SCI is measurable using MRI.