Skip to main content

Atlas-Based Segmentation of Tumor-Bearing Brain Images

  • Chapter
  • First Online:
Tumors of the Central Nervous System, Volume 12

Part of the book series: Tumors of the Central Nervous System ((TCNS,volume 12))

  • 1340 Accesses

Abstract

In diagnostic neuroradiology as well as in radiation oncology and neurosurgery, there is an increasing demand for accurate segmentation of tumor-bearing brain images. Atlas-based segmentation is an appealing automatic technique thanks to its robustness and versatility. However, atlas-based segmentation of tumor-bearing brain images is challenging due to the confounding effects of the tumor in the patient image. In this article, we provide a brief background on brain tumor imaging and introduce the clinical perspective, before we categorize and review the state of the art in the current literature on atlas-based segmentation for tumor-bearing brain images. We also present selected methods and results from our own research in more detail. Finally, we conclude with a short summary and look at new developments in the field, including requirements for future routine clinical use.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Bach-Cuadra M, Pollo C, Bardera A, Cuisenaire O, Villemure JG, Thiran JP (2004) Atlas-based segmentation of pathological MR brain images using a model of lesion growth. IEEE Trans Med Imaging 23:1301–1314

    Article  Google Scholar 

  • Bach-Cuadra M, De Craene M, Duay V, Macq B, Pollo C, Thiran JP (2006) Dense deformation field estimation for atlas-based segmentation of pathological MR brain images. Comput Meth Progr Biomed 84:66–75

    Article  CAS  Google Scholar 

  • Bauer S, Nolte LP, Reyes M (2011a) Segmentation of brain tumor images based on atlas-registration combined with a Markov-Random-Field lesion growth model. Int Symp Biomed Imaging 8:2018–2021

    Google Scholar 

  • Bauer S, Nolte LP, Reyes M (2011b) Fully automatic segmentation of brain tumor images using support vector machine classification in combination with hierarchical conditional random field regularization. Lect Notes Comput Sci 6893:354–361

    Article  Google Scholar 

  • Bauer S, May C, Dionysiou D, Stamatakos G, Büchler P, Reyes M (2012) Multi-scale modeling for image analysis of brain tumor studies. IEEE Trans Biomed-Eng 59:25–29

    Article  PubMed  Google Scholar 

  • Bauer S, Lu H, May CP, Nolte L-P, Büchler P, Reyes M (2013) Integrated segmentation of brain tumor images for radiotherapy and neurosurgery. Int J Imaging Syst Technol 23(1):59–63

    Article  Google Scholar 

  • Brett M, Leff AP, Rorden C, Ashburner J (2001) Spatial normalization of brain images with focal lesions using cost function masking. Neuroimage 14:486–500

    Article  CAS  PubMed  Google Scholar 

  • Cabezas M, Oliver A, Lladó X, Freixenet J, Bach-Cuadra M (2011) A review of atlas-based segmentation for magnetic resonance brain images. Comput Meth Progr Biomed 104:58–77

    Article  Google Scholar 

  • Chitphakdithai N, Duncan JS (2010) Non-rigid registration with missing correspondences in preoperative and postresection brain images. Lect Notes Comput Sci 6361:367–374

    Article  Google Scholar 

  • Commowick O, Stefanescu R, Fillard P, Arsigny V, Ayache N, Pennec X, Malandain G (2005) Incorporating statistical measures of anatomical variability in atlas-to-subject registration for conformal brain radiotherapy. Lect Notes Comput Sci 3750:927–934

    Article  Google Scholar 

  • Dawant BM, Hartmann SL, Pan S, Gadamsetty S (2002) Brain atlas deformation in the presence of small and large space-occupying tumors. Comput Aided Surg 7:1–10

    Article  CAS  PubMed  Google Scholar 

  • DeAngelis LM (2001) Brain tumors. N Engl J Med 344:114–123

    Article  CAS  PubMed  Google Scholar 

  • Deeley MA, Chen A, Datteri R, Noble JH, Cmelak AJ, Donnelly EF, Malcolm AW, Moretti L, Jaboin J, Niermann K, Yang ES, Yu DS, Yei F, Koyama T, Ding GX, Dawant BM (2011) Comparison of manual and automatic segmentation methods for brain structures in the presence of space-occupying lesions: a multi-expert study. Phys Med Biol 56:4557–4577

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Drevelegas A, Papanikolaou N (2011) Imaging modalities in brain tumors. Imag Brain Tumors Histol Corr 13–34

    Google Scholar 

  • Gooya A, Biros G, Davatzikos C (2011a) Deformable registration of glioma images using EM algorithm and diffusion reaction modeling. IEEE Trans Med Imaging 30:375–390

    Article  PubMed Central  PubMed  Google Scholar 

  • Gooya A, Pohl K, Bilello M, Biros G, Davatzikos C (2011b) Joint segmentation and deformable registration of brain scans guided by a tumor growth model. Lect Notes Comput Sci 6892:532–540

    Article  Google Scholar 

  • Ibanez L, Schroeder W, Ng L, Cates J (2005) The ITK software guide 2nd ed., Kitware

    Google Scholar 

  • Isambert A, Dhermain F, Bidault F, Commowick O, Bondiau PY, Malandain G, Lefkopoulos D (2008) Evaluation of an atlas-based automatic segmentation software for the delineation of brain organs at risk in a radiation therapy clinical context. Radiother Oncol 87:93–99

    Article  PubMed  Google Scholar 

  • Kyriacou SK, Davatzikos C, Zinreich SJ, Bryan RN (1999) Nonlinear elastic registration of brain images with tumor pathology using a biomechanical model. IEEE Trans Med Imaging 18:580–592

    Article  CAS  PubMed  Google Scholar 

  • Mang A, Schnabel JA, Crum WR, Modat M, Camara-Rey O, Palm C, Caseiras GB, Jäger HR, Ourselin S, Buzug T, Hawkes DJ (2008) Consistency of parametric registration in serial MRI studies of brain tumor progression. Int J Comput Ass Radiol Surg 3:201–211

    Article  Google Scholar 

  • Marias K, Dionysiou D, Sakkalis V, Graf N, Bohle RM, Coveney PV, Wan S, Folarin A, Büchler P, Reyes M, Clapworthy G, Liu E, Sabczynski J, Bily T, Roniotis A, Tsiknakis M, Kolokotroni E, Giatili S, Veith C, Meese E, Stenzhorn H, Kim YJ, Zasada S, Haidar AN, May C, Bauer S, Zhao Y, Karasek M, Grewer R, Franz A, Stamatakos G (2011) Clinically driven design of multi-scale cancer models: the ContraCancrum project paradigm. J R Soc Interface Focus 1:450–461

    Article  CAS  Google Scholar 

  • May CP, Kolokotroni E, Stamatakos GS, Büchler P (2011) Coupling biomechanics to a cellular level model: an approach to patient-specific image driven multi-scale and multi-physics tumor simulation. Prog Biophys Mol Biol 107:193–199

    Article  PubMed  Google Scholar 

  • Mazzara GP, Velthuizen RP, Pearlman JL, Greenberg HM, Wagner H (2004) Brain tumor target volume determination for radiation treatment planning through automated MRI segmentation. Int J Radiat Oncol 59:300–312

    Article  Google Scholar 

  • Mohamed A, Zacharaki EI, Shen D, Davatzikos C (2006) Deformable registration of brain tumor images via a statistical model of tumor-induced deformation. Med Image Anal 10:752–763

    Article  PubMed  Google Scholar 

  • Niethammer M, Hart GL, Pace DF, Vespa PM, Irimia A, van Horn JD, Aylward SR (2011) Geometric metamorphosis. Lect Notes Comput Sci 6892:639–646

    Article  Google Scholar 

  • Pham DL, Xu C, Prince JL (2000) Current methods in medical image segmentation. Annu Rev Biomed Eng 2:315–337

    Article  CAS  PubMed  Google Scholar 

  • Prastawa M, Bullitt E, Gerig G (2009) Simulation of brain tumors in MR images for evaluation of segmentation efficacy. Med Image Anal 13:297–311

    Article  PubMed Central  PubMed  Google Scholar 

  • Rohlfing T, Zahr NM, Sullivan EV, Pfefferbaum A (2010) The SRI24 multichannel atlas of normal adult human brain structure. Hum Brain Mapp 31:798–819

    Article  PubMed Central  PubMed  Google Scholar 

  • Speier W, Iglesias J, El-Kara L, Tu Z, Arnold C (2011) Robust skull stripping of clinical glioblastoma multiforme data. Lect Notes Comput Sci 6893:659–666

    Article  Google Scholar 

  • Stamatakos GS, Kolokotroni E, Dionysiou D, Georgiadi E, Desmedt C (2010) An advanced discrete state-discrete event multiscale simulation model of the response of a solid tumor to chemotherapy: mimicking a clinical study. J Theor Biol 266:124–139

    Article  CAS  PubMed  Google Scholar 

  • Stefanescu R, Commowick O, Malandain G, Bondiau PY, Ayache N, Pennec X (2004) Non-rigid atlas to subject registration with pathologies for conformal brain radiotherapy. Lect Notes Comput Sci 3216:704–711

    Article  Google Scholar 

  • Vercauteren T, Pennec X, Perchant A, Ayache N (2009) Diffeomorphic demons: efficient non-parametric image registration. Neuroimage 45:S61–S72

    Article  PubMed  Google Scholar 

  • Zacharaki EI, Shen D, Lee SK, Davatzikos C (2008) ORBIT: a multiresolution framework for deformable registration of brain tumor images. IEEE Trans Med Imaging 27:1003–1017

    Article  PubMed Central  PubMed  Google Scholar 

  • Zacharaki EI, Hogea CS, Shen D, Biros G, Davatzikos C (2009) Non-diffeomorphic registration of brain tumor images by simulating tissue loss and tumor growth. Neuroimage 46:762–774

    Article  PubMed Central  PubMed  Google Scholar 

  • Zitova B, Flusser J (2003) Image registration methods: a survey. Image Vision Comput 21:977–1000

    Article  Google Scholar 

Download references

Acknowledgements

This work was partially funded by the European Union within the framework of the ContraCancrum project (FP7 – IST-223979).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefan Bauer .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media Dordrecht

About this chapter

Cite this chapter

Bauer, S., Wiest, R., Slotboom, J., Reyes, M. (2014). Atlas-Based Segmentation of Tumor-Bearing Brain Images. In: Hayat, M. (eds) Tumors of the Central Nervous System, Volume 12. Tumors of the Central Nervous System, vol 12. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7217-5_14

Download citation

  • DOI: https://doi.org/10.1007/978-94-007-7217-5_14

  • Published:

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-94-007-7216-8

  • Online ISBN: 978-94-007-7217-5

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics