Smart histogram analysis applied to the skull-stripping problem in T1-weighted MRI

Computers in Biology and Medicine

Volumn 42, Issue 5, 2012, Pages 509-522

  Balan, André G R ^a   Traina, Agma J M ^b   Ribeiro, Marcela X ^c   Marques, Paulo M A ^b   Traina Jr , Caetano ^b  

^a UNIVERSIDADE FEDERAL DO ABC   (Brazil)

^b UNIVERSITY OF SÃO PAULO   (Brazil)

^c FEDERAL UNIVERSITY OF SÃO CARLOS   (Brazil)

Author keywords

Binary morphology; Brain; Histogram analysis; Image segmentation; MRI; Skull stripping

Indexed keywords

BINARY MORPHOLOGY; DATA SETS; FUNDAMENTAL COMPONENT; GAUSSIAN FITS; HISTOGRAM ANALYSIS; IMAGE DATABASE; MR IMAGES; NOISE RATIO; PARAMETER-TUNING; SKULL-STRIPPING;

BRAIN; GRAPHIC METHODS; IMAGE SEGMENTATION; MAGNETIC RESONANCE IMAGING;

THREE DIMENSIONAL;

ALGORITHM; ANALYTIC METHOD; ARTICLE; BRAIN EXTRACTION TOOL; BRAIN SURFACE EXTRACTOR; DATA BASE; HISTOGRAM; HUMAN; NUCLEAR MAGNETIC RESONANCE IMAGING; PRIORITY JOURNAL; SIGNAL NOISE RATIO;

ALGORITHMS; DATABASE MANAGEMENT SYSTEMS; HUMANS; MAGNETIC RESONANCE IMAGING; SKULL;

EID: 84859210948     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2012.01.004     Document Type: Article

References (33)

1. A.G.R. Balan, A.J.M. Traina, M.X. Ribeiro, P.M.A. Marques, C. Traina Jr, HEAD: the human encephalon automatic delimiter, in: Proceedings of the 20th IEEE International Symposium on Computer-Based Medical Systems, Maribor, Slovenia, pp. 171-176.
2. Guttmann C.R., Jolesz F.A., Kikinis R., Killiany R.J., Moss M.B., Sandor T., Albert M.S. White matter changes with normal aging. Neurology 1998, 50:972-978.
3. Lee J.W., Reutens D.C., Dubeau F., Evans A., Andermann F. Morphometry in temporal lobe epilepsy. Magn. Reson. Imaging 1995, 13:1073-1080.
4. D. Dean, P. Buckley, F.L. Bookstein, J. Kamath, D. Kwon, L. Friedman, C. Lys, Three dimensional MR-based morphometric comparison of schizophrenic and normal cerebral ventricles, in: Proceedings of the 4th International Conference on Visualization in Biomedical Computing (VBC 1996), vol. 1131, Hamburg, Germany, 1996, pp. 363-372.
5. Jackson E., Narayana P., Wolinsky J., Doyle T. Accuracy and reproducibility in volumetric analysis of multiple. J. Comput. Assisted Tomography 1993, 17:200-205.
6. A. Elbaz, M.F. Casanova, G. Gimelfarb, M. Mott, A.E. Switwala, A new image analysis approach for automatic classification of autistic brains, in: Proceedings of the 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2007), Washington DC, USA, pp. 352-355.
7. Sandor S., Leahy R.M. Surface-based labeling of cortical anatomy using a deformable atlas. IEEE Trans. Med. Imaging 1997, 16:41-54.
8. Smith S.M. Fast robust automated brain extraction. Hum. Brain Mapp. 2002, 17:143-155.
9. Tan P.-N., Steinbach M., Kumar V. Introduction to Data Mining 2005, Addison-Wesley.
10. Lemieux L., Hagemann G., Krakow K., Woermann F.G. Fast, accurate, and reproducible automatic segmentation of the brain in T1-weighted volume MRI data. Magn. Reson. Med. 1999, 42:127-135.
11. Atkins M.S., Mackiewich B.T. Fully automatic segmentation of the brain in MRI. IEEE Trans. Med. Imaging 1998, 17:98-107.
12. B.D. Ward, Intracranial Segmentation, Technical Report, Biophysics Research Institute, Medical College of Wisconsin, 1999.
13. Stokking R., Vincken K.L., Viergever M.A. NeuroImage 2000, 12:726-738.
14. Hata Y., Kobashi S., Hirano S., Kitagaki H., Mori E. Automated segmentation of human brain MR images aided by fuzzy information granulation and fuzzy inference. IEEE Trans. Syst. Man Cybern. Part C: Appl. Rev. 2000, 30:381-395.
15. Kass M., Witkin A., Terzopoulos D. Snakes: active contour models. Int. J. Comput. Vision 1987, 1:321-331.
16. Sadananthan S.A., Zheng W., Chee M.W., Zagorodnov V. Skull stripping using graph cuts. NeuroImage 2010, 49:225-239.
17. Otsu N. A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 1979, 9:62-66.
18. Sezgin M., Sankur B. Survey over image thresholding techniques and quantitative performance evaluation. J. Electron. Imaging 2004, 13:146-168.
19. Cox R.W. AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput. Biomed. Res. 1996, 29:162-173.
20. Shattuck D.W., Sandor-Leahy S.R., Schaper K.A., Rottenberg D.A., Leahy R.M. Magnetic resonance image tissue classification using a partial volume model. NeuroImage 2001, 13:856-876.
21. Shattuck D.W., Leahy R.M. BrainSuite: an automated cortical surface identification tool. Med. Image Anal. 2002, 6:129-142.
22. Dogdas B., Shattuck D.W., Leahy R.M. Segmentation of skull and scalp in 3-D human MRI using mathematical morphology. Hum. Brain Mapp. 2005, 26:273-285.
23. Fennema-Notestine C., Ozyurt I.B., Clark C.P., Morris S., Bischoff-Grethe A., Bondi M.W., Jernigan T.L., Fischl B., Segonne F., Shattuck D.W., Leahy R.M., Rex D.E., Toga A.W., Zou K.H., Brown G.G. Quantitative evaluation of automated skull-stripping methods applied to contemporary and legacy images: effects of diagnosis, bias correction, and slice location. Hum. Brain Mapp. 2006, 27:99-113.
24. A. Huang, R. Abugharbieh, R. Tam, A. Traboulsee, MRI brain extraction with combined expectation maximization and geodesic active contours, in: Proceedings of the 6th IEEE International Symposium on Signal Processing and Information Technology ISSPIT 2006, Vancouver, BC, Canada, pp. 107-111.
25. Segonne F., Dale A., Busa E., Glessner M., Salat D., Hahn H., Fischl B. A hybrid approach to the skull stripping problem in MRI. NeuroImage 2004, 22:1060-1075.
26. Osher S., Sethian J. Fronts propagating with curvature dependent speed: algorithms based on Hamilton-Jacobi formulation. J. Comput. Phys. 1988, 79:12-49.
27. Zhuang A.H., Valentinoa D.J., Toga A.W. Skull-stripping magnetic resonance brain images using a model-based level set. NeuroImage 2006, 32:79-92.
28. Baillard C., Hellier P., Barillot C. Segmentation of brain 3D MR images using level sets and dense registration. Med. Image Anal. 2001, 5:185-194.
29. Suri J.S. Two-dimensional fast magnetic resonance brain segmentation. IEEE Eng. Med. Biol. Mag. 2001, 20:84-95.
30. Rex D.E., Shattuck D.W., Woods R.P., Narr K.L., Luders E., Rehm K., Stolzner S.E., Rottenberg D.A., Toga A.W. A meta-algorithm for brain extraction in MRI. NeuroImage 2004, 23:625-637.
31. Rehm K., Schaper K., Anderson J., Woods R., Stoltzner S., Rottenberg D. Putting our heads together: a consensus approach to brain/non-brain segmentation in T1-weighted MR volumes. NeuroImage 2004, 22:1262-1270.
32. Boesen K., Rehm K., Schaper K., Stoltzner S., Woods R., Lüders E., Rottenberga D. Quantitative comparison of four brain extraction algorithms. NeuroImage 2004, 22:1255-1261.
33. Cocosco C.A., Kollokian V., Kwan R.K.-S., Pike G.B., Evans A.C. Brainweb: online interface to a 3D MRI simulated brain database. NeuroImage 1997, 5:S425.