RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI
Rodent brain skull-stripping from MRI
RATS is a rapid, robust and highly accurate algorithm for the skull-stripping of the rodent brain from MRI data. It consists of two stages, a mathematical morphology stage for initialization followed by a LOGISMOS-based approach for final segmentation. Please visit the overview page for more details.
The software distribution consists of two (linux64) executables corresponding to each of these stages. An example scan and parameter values for its processing are also included for illustration purposes. RATS is currently not supported on Windows or MacOS. It can read any ITK-compatible image format, and its outputs are in the form of ITK-compatible images and VTK polydata mesh files.
The current release of RATS is available free of charge for research use.
For further details on the algorithm, please refer to the following papers. By using the RATS software, you are obliged to reference these two papers.
- Oguz I, Zhang H, Rumple A, Sonka M. RATS: Rapid Automatic Tissue Segmentation in rodent brain MRI. Journal of neuroscience methods (2014) vol. 221 pp. 175 - 182. http://www.sciencedirect.com/science/article/pii/S0165027013003440
- Yin Y, Zhang X, Williams R, Wu X, Anderson D, Sonka M. LOGISMOS - Layered Optimal Graph Image Segmentation of Multiple Objects and Surfaces: cartilage segmentation in the knee joint. IEEE Transactions on Medical Imaging (2010) vol. 29 (12) pp. 2023-37. http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5512662
Development was supported, in part, by NIH-NIBIB R01-EB044640.