MRI-based synthetic CT generation using semantic random forest with iterative refinement.

Target delineation for radiation therapy treatment planning often benefits from magnetic resonance imaging (MRI) in addition to x-ray computed tomography (CT) due to MRI's superior soft tissue contrast. MRI-based treatment planning could reduce systematic MR-CT co-registration errors, medical cost, radiation exposure, and simplify clinical workflow. However, MRI-only based treatment planning is not widely used to date because treatment-planning systems rely on the electron density information provided by CTs to calculate dose. Additionally, air and bone regions are difficult to separategiven their similar intensities in MR imaging. The purpose of this work is to develop a learning-based method to generate patient-specific synthetic CT (sCT) from a routine anatomical MRI for use in MRI-only radiotherapy treatment planning. An auto-context model with patch-based anatomical features was integrated into a classification random forest to generate and improve semantic information. The semantic information along with anatomical features was then used to train a series of regression random forests based on the auto-context model. After training, the sCT of a new MRI can be generated by feeding anatomical features extracted from the MRI into the well-trained classification and regression random forests. The proposed algorithm was evaluated using 14 patient datasets withT1-weighted MR and corresponding CT images of the brain. The mean absolute error (MAE), peak signal-to-noise ratio (PSNR), and normalized cross correlation (NCC) were 57.45  ±  8.45 HU, 28.33  ±  1.68 dB, and 0.97  ±  0.01. We also compared the difference between dose maps calculated on the sCT and those on the original CT, using the same plan parameters. The average DVH differences among all patients are less than 0.2 Gy for PTVs, and less than 0.02 Gy for OARs. The sCT generation by the proposed method allows for dose calculation based MR imaging alone, and may be a useful tool for MRI-based radiation treatment planning.