References for Smooth functions and Region of Interest functions

1. A.K. Jain, Fundamentals of Digital Image Processing, Prentice Hall, Englewood Cliffs, New Jersey, 1989.

2. W.K. Pratt, Digital Image Processing, John Wiley & Sons, Inc. New York, 1978.

References for Iso-Data

1. H. Soltanian-Zadeh, J.P. Windham, and L. Robbins: "Semi-Supervised Segmentation of MRI Stroke Studies." Presented at and Published in the Proceedings of SPIE Medical Imaging 1997: Image Processing Conference, Newport Beach, CA, Feb. 1997.

2. K.M.A. Welch, J.P. Windham, R. Knight, V. Nagesh, J. Hugg, M. Jacobs, D.J. Peck, P. Booker, M. Dereski, S. Levine, ``A Model to Predict the Histopathology of Human Stroke Using Diffusion and T2-Weighted Magnetic Resonance Imaging,'' Stroke, vol. 26, pp. 1983-1989, 1995.

3. K. Takahashi, H. Nakatani, and K. Abe, ``Color image segmentation using ISODATA clustering method,'' Proceedings of Second Asian Conference on Computer Vision, vol. 1, pp. 523-527, 1995.

4. Jacobs, M. A., Knight, R. A., Soltanian-Zadeh, H., Zheng, Z. G., Goussev, A. V., Peck, D. J., Windham, J. P., and Chopp, M. "Unsupervised segmentation of multiparameter MRI in experimental cerebral ischemia with comparison to T2, diffusion, and ADC MRI parameters and histopathological validation," Journal of Magnetic Resonance Imaging. 11: 425-37, 2000.

5. Nagesh, V., Welch, K. M., Windham, J. P., Patel, S., Levine, S. R., Hearshen, D., Peck, D., Robbins, K., D'Olhaberriague, L., Soltanian-Zadeh, H., and Boska, M. D. "Time course of ADCw changes in ischemic stroke: beyond the human eye," Stroke. 29: 1778-82, 1998.
    

References for the Multi-Wavelet Texture function

1. R. Nezafat and H. Soltanian-Zadeh: "Multiwavelet Based Feature Extraction for MRI Segmentation." Presented at and Published in the Proceedings of SPIE Annual Meeting, San Diego, CA, July 1998.

2. H. Soltanian-Zadeh, R. Nezafat, and J.P. Windham: "Is There Texture Information in Standard Brain MRI?" Presented at and Published in the Proceedings of SPIE Medical Imaging 1999: Image Processing Conference, San Diego, CA, Feb. 1999.
    

References for Region of Interest Thresholds

1. J.S. Weszka, ``A survey of threshold selection techniques,'' Comput. Graphics Image Process., vol. 7, pp. 259-265, 1978.

2. R. Kohler, ``A segmentation system based on thresholding,'' Comput. Graphics Image Process., vol. 15, pp. 319-337, 1981.

References for Contour regions of interest for Registration

1. H. Soltanian-Zadeh and J.P. Windham: "A Multi-resolution Approach for Intracranial Volume Segmentation from Brain Images." Medical Physics, vol. 24, no. 12, pp. 1844-1853, Dec. 1997.

References for the Automated Image Registration Program from UCLA (web site):

1. Woods RP, Cherry SR, Mazziotta JC. Rapid automated algorithm for aligning and reslicing PET images. Journal of Computer Assisted Tomography 1992;16:620-633.

   The original AIR manuscript validating the intramodality method implemented in AIR 1.0.

2. Woods RP, Mazziotta JC, Cherry SR. MRI-PET registration with automated algorithm. Journal of Computer Assisted Tomography 1993;17:536-546.

   The method used for intermodality registration as implemented in AIR 1.0

3. Woods RP, Grafton ST, Holmes CJ, Cherry SR, Mazziotta JC. Automated image registration: I. General methods and intrasubject, intramodality validation. Journal of Computer Assisted Tomography 1998;22:141-154.

   Description of AIR 3.0 and validation for intrasubject, intramodality registration of MRI data and intrasubject, intramodality registration of PET data.

4. Woods RP, Grafton ST, Watson JDG, Sicotte NL, Mazziotta JC. Automated image registration: II. Intersubject validation of linear and nonlinear models. Journal of Computer Assisted Tomography 1998;22:155-165.

   Validation of AIR 3.0 for intersubject registration.

References for the CTN software package from the Mallinkrodt Institute of Radiology (web site, ftp download)

1. Moore, S.M., Hoffman, S.A., Beecher, D.E., "DICOM Shareware: A Public Implementation of the DICOM Standard," in Medical Imaging 1994-PACS: Design and Evaluation, R. Gilbert Jost, Editor, Proc SPIE 2165, pp. 772-781 (1994)

References for Mutual Information Registration

1. F. Maes, A. Collignon, D. Vandermeulen, G. Marchal, and P. Suetens "Multimodality Image Registration by Maximization of Mutual Information," IEEE Transactions on Medical Imaging. Vol. 16, No. 2, pp. 187-198, April 1997.

References for use of Registration and Warping

1. Jacobs, M., Windham, J., Soltanian-Zadeh, H., Peck, D., and Knight RA "Registration and Warping of Magnetic Resonance Images to Histological Sections," Medical Physics. 26: 1-11, 1999.

2. Jacobs, M. A., Windham, J. P., Soltanian-Zadeh, H., Peck, D. J., and Knight, R. A. "Registration and warping of magnetic resonance images to histological sections," Medical Physics. 26: 1568-78, 1999.

3. Pelizzari, C. A., Chen, G. T., Spelbring, D. R., Weichselbaum, R. R., and Chen, C. T. "Accurate three-dimensional registration of CT, PET, and/or MR images of the brain," Journal of Computer Assisted Tomography. 13: 20-6, 1989.

References for Warping calculation method (Bookstein's)

1. F.L. Bookstein, ``Principal Warps: Thin-Plate Splines and the Decomposition of Deformations,'' IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 11, no. 6, pp. 567-585, 1989.

References for Restoration

1. Soltanian-Zadeh, H., Windham, J. P., and Yagle, A. E. "A Multidimensional Nonlinear Edge-Preserving Filter for Magnetic Resonance Image Restoration," IEEE Transaction in Image Processing. 4: 147-161, 1995.

References for the Eigen Segmentation Filter

1. Soltanian-Zadeh, H., Windham, J. P., and Jenkins, J. M. "Error propagation in Eigenimage Filtering," IEEE Transaction in Medical Imaging. 9: 405-420, 1990.

2. Soltanian-Zadeh, H., Saigal, R., Windham, J. P., Yagle, A. E., and Hearshen, D. O. "Optimization of MRI Protocols and Pulse Sequence Parameters for Eigenimage Filtering," IEEE Transaction in Medical Imaging. 13: 161-175, 1994.

3. Windham, J. P., Abd-Allah, M. A., Reimann, D. A., Froelich, J. W., and Haggar, A. M. "Eigenimage filtering in MR imaging," Journal of Computer Assisted Tomography. 12: 1-9, 1988.

4. Peck, D. J., Windham, J. P., Soltanian-Zadeh, H., and Roebuck, J. R. "A fast and accurate algorithm for volume determination in MRI," Medical Physics. 19: 599-605, 1992.

5. Peck, D. J., Windham, J. P., Emery, L. L., Soltanian-Zadeh, H., Hearshen, D. O., and Mikkelsen, T. "Cerebral tumor volume calculations using planimetric and eigenimage analysis," Medical Physics. 23: 2035-42, 1996.

6. H. Soltanian-Zadeh, J.P. Windham, and A.E. Yagle: "Optimal Transformation for Correcting Partial Volume Averaging Effects in Magnetic Resonance Imaging." IEEE Trans. Nuc. Sci., vol. 40, No. 4, pp. 1204-1212, Aug. 1993.

References for the Difference Segmentation Filter

1. H. Soltanian-Zadeh, J.P. Windham, D.J. Peck, and A.E. Yagle: "A Comparative Analysis of Several Transformations for Enhancement and Segmentation of Magnetic Resonance Image Scene Sequences." IEEE Trans. Med. Imag., vol. 11, no. 3, pp. 302-318, Sept. 1992.

References for the Max-Min CNR Segmentation Filter

1. H. Soltanian-Zadeh and J.P. Windham: "Novel and General Approach to Linear Filter Design for CNR Enhancement of MR Images with Multiple Interfering Features in the Scene." Journal of Electronic Imaging, vol. 1, no. 2, pp. 171-182, April 1992.

References for the Target Point and Location Variant functions

1. H. Soltanian-Zadeh, J.P. Windham, D.J. Peck, and A.E. Yagle: "A Comparative Analysis of Several Transformations for Enhancement and Segmentation of Magnetic Resonance Image Scene Sequences." IEEE Trans. Med. Imag., vol. 11, no. 3, pp. 302-318, Sept. 1992.

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