Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

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Brain tumor segmentation and characterisation

In medical collaboration with:
Klinikum rechts der Isar der TU München, Neuroradiologie: Prof. Dr. med. Claus Zimmer and Priv.-Doz. Dr. med. Jan Stefan Bauer

Scientific Director: Prof. Dr. Bjoern Menze

Contact Person(s): Esther Alberts

Keywords: IBBM: image computing


A generative-discriminative framework is built for multi-modal brain tumor segmentation with the use of longitudinal growth models. The framework will be validated and compared with the state-of-the-art. In a later stage, image features based on tumor-specific bio-markers are explored, and, more specifically, their contribution to more accurate brain tumor segmentation is studied.

Detailed Project Description

Data acquisition and pre-processing
We use MR images of four modalities: T1, T1c, T2 and FLAIR. Images are pre-processed by means of ITK MR biasfield correction and NiftiReg non-rigid registrations.

Image segmentation techniques
We use a generative tumor segmentation algorithm based on Expectation-Maximisation, which calculates spatial tumor probability maps for every modality. These tumor probability maps are subsequently spatially and temporally regularized using a 4-dimensional Markov random field solved by graph cut.

Patient-specific tumor growth estimations
A non-parametric growth model is build on top of the graph cut segmentations and estimates tumor volumes along time.


Figure 1: Temporal series of a growing brain tumor segmented out of a temporal FLAIR series with scan intervals of about one month.
Figure 2: Outline of an algorithm segmenting temporal brain MR scans, calculating tumor volumes and estimating tumor growth or shrinkage in between all time points.
Figure 3: Outline of an algorithm segmenting temporal brain MR scans and calculating tumor volumes with an additional quantification of volumetric uncertainties based on Gumbel perturbations.

Clinical Relevance

Oncology, Neuroradiology


Contact Person(s)

Esther Alberts
M.Sc. Esther Alberts

Working Group

Bjoern Menze
Prof. Bjoern Menze
Esther Alberts
M.Sc. Esther Alberts


Technische Universität München
Institut für Informatik / I16
Boltzmannstr. 3
85748 Garching bei München

Tel.: +49 89 289-17058
Fax: +49 89 289-17059
Visit our lab at Garching.

Klinikum rechts der Isar
der Technischen Universitüt München
Ismaninger Str. 22
81675 München

IFL Lab - Room: 01.3a-c
Tel.: +49 89 4140-6457
Fax: +49 89 4140-6458
Visit our lab at Klinikum rechts der Isar.

internal project page

Please contact Esther Alberts for available student projects within this research project.

Edit | Attach | Refresh | Diffs | More | Revision r1.1 - 18 Mar 2015 - 11:39 - EstherAlberts

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