Fully automatic 3D segmentation of the thoracolumbar spinal cord and the vertebral canal from T2-weighted MRI using K-means clustering algorithm

Research output: Contribution to journalArticlepeer-review


  • Sahar Sabaghian
  • Hamed Dehghani
  • Seyed Amir Hossein Batouli
  • Ali Khatibi
  • Mohammad Ali Oghabian


Study design

Method development.


To develop a reliable protocol for automatic segmentation of Thoracolumbar spinal cord using MRI based on K-means clustering algorithm in 3D images.


University-based laboratory, Tehran, Iran.


T2 structural volumes acquired from the spinal cord of 20 uninjured volunteers on a 3T MR scanner. We proposed an automatic method for spinal cord segmentation based on the K-means clustering algorithm in 3D images and compare our results with two available segmentation methods (PropSeg, DeepSeg) implemented in the Spinal Cord Toolbox. Dice and Hausdorff were used to compare the results of our method (K-Seg) with the manual segmentation, PropSeg, and DeepSeg.


The accuracy of our automatic segmentation method for T2-weighted images was significantly better or similar to the SCT methods, in terms of 3D DC (p < 0.001). The 3D DCs were respectively (0.81 ± 0.04) and Hausdorff Distance (12.3 ± 2.48) by the K-Seg method in contrary to other SCT methods for T2-weighted images.


The output with similar protocols showed that K-Seg results match the manual segmentation better than the other methods especially on the thoracolumbar levels in the spinal cord due to the low image contrast as a result of poor SNR in these areas.


Original languageEnglish
JournalSpinal Cord
Publication statusPublished - 4 Mar 2020