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.

Development was supported, in part, by NIH-NIBIB R01-EB044640.

Please visit the FAQ page and/or contact milan-sonka@uiowa.edu for any questions and feedback.

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Please fill the information form below to request access to software download links.

Definitions:
 
Provider - Institution providing the Original Material:
        The University of Iowa Research Foundation
Provider's Scientists:
        Ipek Oguz
        Xiaodong Wu
        Milan Sonka
 
Recipient - Institution receiving the Original Material:
        Institution employing person requesting download: xxxxx
 
Recipient's Scientist(s): xxxxx
 
Person requesting download: xxxxx
 
Software: Iowa Reference Algorithms, including:
        RATS_MM
        RATS_LOGISMOS
        All which are partially described in:
Kang L, Wu X, Chen DZ, Sonka M. Optimal Surface Segmentation in Volumetric Images - A Graph-Theoretic Approach. IEEE Transactions on Pattern Analysis and Machine Intelligence Volume 28:119-134, 2006. doi:10.1109/TPAMI.2006.19
Yin Y, Zhang X, Williams R, Wu X, Anderson DD, 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. 
doi:10.1109/TMI.2010.2058861
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.
doi:10.1016/j.jneumeth.2013.09.021

Patents
United States Patent 7,995,810, "System and Methods for Image segmentation in N- dimensional space". Inventors: K Li, X Wu, DZ Chen, M Sonka
And any other patents and applications claiming priority to the above.
 
Terms and Conditions of this Agreement
1. The Effective Date of this Software Transfer Agreement is the date electronically agreed to by Recipient's Scientist as part of this license.
2. The Software is the property of Provider and is to be used by Recipient solely for research purposes only at Recipient's institution and only under the direction of the Recipient's Scientist(s). The Software may not be used in the diagnosis or treatment of patients and Recipient and Recipient Scientist(s) may not use Software in a manner which generates income or remuneration for Recipient and Recipient Scientist(s).
3. The Recipient's Scientist(s) agrees not to transfer or provide the Software to anyone else at Recipient's institution or any third party without the prior written consent of Provider. The Software being used is further restricted to a single computer. Recipient's Scientist shall refer any request for the Software to Provider.
4. No rights are provided to Recipient under the patents above or any patents, patent applications, copyrights, trade secrets or other proprietary rights of Provider. In particular, no rights are provided to use the Software or any related intellectual property of Provider for making, using, or distributing the intellectual property, material or derivatives thereof in exchange for any form of compensation or reimbursement. However, nothing in this paragraph or any other section of this Agreement shall be construed to interfere with, restrict or otherwise limit Recipient's rights to receive or spend the grant proceeds under any Prime Award and Provider encourages Recipient to explore state, Federal and internal funding opportunities using the Software.
5. The provision of the Software to Recipient shall not alter any preexisting right to the Software, including the customary rights granted to the federal government or non-profit foundations.
6. Any Software delivered pursuant to this Agreement is understood to be experimental in nature. PROVIDER MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS.
7. Except to the extent prohibited by law, Recipient assumes all liability for damages which may arise from its use, storage or disposal of the Software. Provider will not be liable to Recipient for any loss, claim or demand made by Recipient, made against Recipient or by any other party, due to or arising from the use of the Software by the Recipient, except to the extent permitted by law when caused by the gross negligence or willful misconduct of Provider.
8. Software is being provided to Recipient at no cost.
9. Recipient agrees that Provider and Provider's Scientist(s) shall receive appropriate recognition in any publication or presentation resulting from the use of agreed upon Software.
10. Recipient agrees to use the Software in compliance with all applicable statues and regulations, including, for example, Export Control.
 
Institution: The University of Iowa Research Foundation
Address: 200 S. Capitol Street, 2660 University Capitol Centre, Iowa City, IA 52242-5500
Authorized Official: Zev Sunleaf
Title: Executive Director
 
 

Read Terms Agreement

Definitions:
 
Provider - Institution providing the Original Material:
        The University of Iowa Research Foundation
Provider's Scientists:
        Ipek Oguz
        Xiaodong Wu
        Milan Sonka
 
Recipient - Institution receiving the Original Material:
        Institution employing person requesting download: xxxxx
 
Recipient's Scientist(s): xxxxx
 
Person requesting download: xxxxx
 
Software: Iowa Reference Algorithms, including:
        RATS_MM
        RATS_LOGISMOS
        All which are partially described in:
Kang L, Wu X, Chen DZ, Sonka M. Optimal Surface Segmentation in Volumetric Images - A Graph-Theoretic Approach. IEEE Transactions on Pattern Analysis and Machine Intelligence Volume 28:119-134, 2006. doi:10.1109/TPAMI.2006.19
Yin Y, Zhang X, Williams R, Wu X, Anderson DD, 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. 
doi:10.1109/TMI.2010.2058861
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.
doi:10.1016/j.jneumeth.2013.09.021

Patents
United States Patent 7,995,810, "System and Methods for Image segmentation in N- dimensional space". Inventors: K Li, X Wu, DZ Chen, M Sonka
And any other patents and applications claiming priority to the above.
 
Terms and Conditions of this Agreement
1. The Effective Date of this Software Transfer Agreement is the date electronically agreed to by Recipient's Scientist as part of this license.
2. The Software is the property of Provider and is to be used by Recipient solely for research purposes only at Recipient's institution and only under the direction of the Recipient's Scientist(s). The Software may not be used in the diagnosis or treatment of patients and Recipient and Recipient Scientist(s) may not use Software in a manner which generates income or remuneration for Recipient and Recipient Scientist(s).
3. The Recipient's Scientist(s) agrees not to transfer or provide the Software to anyone else at Recipient's institution or any third party without the prior written consent of Provider. The Software being used is further restricted to a single computer. Recipient's Scientist shall refer any request for the Software to Provider.
4. No rights are provided to Recipient under the patents above or any patents, patent applications, copyrights, trade secrets or other proprietary rights of Provider. In particular, no rights are provided to use the Software or any related intellectual property of Provider for making, using, or distributing the intellectual property, material or derivatives thereof in exchange for any form of compensation or reimbursement. However, nothing in this paragraph or any other section of this Agreement shall be construed to interfere with, restrict or otherwise limit Recipient's rights to receive or spend the grant proceeds under any Prime Award and Provider encourages Recipient to explore state, Federal and internal funding opportunities using the Software.
5. The provision of the Software to Recipient shall not alter any preexisting right to the Software, including the customary rights granted to the federal government or non-profit foundations.
6. Any Software delivered pursuant to this Agreement is understood to be experimental in nature. PROVIDER MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED. THERE ARE NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT THE USE OF THE MATERIAL WILL NOT INFRINGE ANY PATENT, COPYRIGHT, TRADEMARK OR OTHER PROPRIETARY RIGHTS.
7. Except to the extent prohibited by law, Recipient assumes all liability for damages which may arise from its use, storage or disposal of the Software. Provider will not be liable to Recipient for any loss, claim or demand made by Recipient, made against Recipient or by any other party, due to or arising from the use of the Software by the Recipient, except to the extent permitted by law when caused by the gross negligence or willful misconduct of Provider.
8. Software is being provided to Recipient at no cost.
9. Recipient agrees that Provider and Provider's Scientist(s) shall receive appropriate recognition in any publication or presentation resulting from the use of agreed upon Software.
10. Recipient agrees to use the Software in compliance with all applicable statues and regulations, including, for example, Export Control.
 
Institution: The University of Iowa Research Foundation
Address: 200 S. Capitol Street, 2660 University Capitol Centre, Iowa City, IA 52242-5500
Authorized Official: Zev Sunleaf
Title: Executive Director