Multi-class brain segmentation using atlas propagation and EM-based refinement

Christian Ledig, Robin Wolz, Paul Aljabar, Jyrki Lötjönen, Rolf Heckemann, Alex Hammers, Daniel Rueckert

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingsScientificpeer-review

28 Citations (Scopus)


In recent years, multi-atlas segmentation has emerged as one of the most accurate techniques for the segmentation of brain magnetic resonance (MR) images, especially when combined with intensity-based refinement techniques such as graph-cut or expectation-maximization (EM) optimization. However, most of the work so far has focused on intensity-based refinement strategies for individual anatomical structures such as the hippocampus. In this work we extend a previously proposed framework for labeling whole brain scans by incorporating a global and stationary Markov random field that ensures the consistency of the neighbourhood relations between structures with an a-priori defined model. In particular we improve the segmentation result of a locally weighted multi-atlas fusion method for 41 different structures simultaneously by applying a subsequent EM optimization step. We evaluate the proposed approach on 30 manually annotated brain MR images and observe an improvement of label overlaps to a manual reference by up to 6%. We also achieved a considerably improved group separation when the proposed segmentation framework is applied to a volumetric analysis of 404 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort.
Original languageEnglish
Title of host publication2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)
PublisherIEEE Institute of Electrical and Electronic Engineers
ISBN (Electronic)978-1-4577-1858-8, 978-1-4577-1856-4
ISBN (Print)978-1-4577-1857-1
Publication statusPublished - 2012
MoE publication typeA4 Article in a conference publication
Event9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012 - Barcelona, Spain
Duration: 2 May 20125 May 2012
Conference number: 9


Conference9th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI 2012
Abbreviated titleISBI 2012


  • brain atrophy
  • hippocampus
  • Alzheimers disease


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