TeachingSs14ImageBasedBiomedicalModeling

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

Hauptseminar/Master Seminar:
Image-based Biomedical Modeling

Bjoern Menze (TUM), Dana Cobzas (U Alberta), Kuangyu Shi (TUM Klinikum Rechts der Isar), Vladimir Golkov (GE), Michael Kelm (Siemens)

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Type: Master Seminar Module IN2107
SWS: 2+0
ECTS: 4 Credits
Location: 03.13.010 (NB: will be 01.16.020 on April 9th and May 7th)
Time: 10.00-12.00
Course Language: English

Content

Many clinical imaging sequences include image modalities that provide unique insights into the human body: describing blood flow pattern or water diffusion, visualizing micro-structural tissue properties, or quantifying metabolic processes that have been found to be relevant for specific diseases. To access and explore the rich biological information of such multimodal CT, PET, and MR image data sets, different approaches from biophysical modeling and computational physiology are used.

The topic of this seminar is to survey such computational models by reading, discussing and understanding key publications in this field, for example, on:

  • spatial atlases that encode the variation of anatomy throughout the population in a probabilistic fashion,
  • dynamical models that describe blood flow patterns in MR and CT, or the the dynamics of metabolic pathways as measured via PET,
  • spatio-temporal models that describe cardiac electro-physiological excitations, or the growth patterns of tumors,
  • global probabilistic models that relate image features with clinical information or genetic variables.

Optional: Some of the topics will allow the presenter to use related software tools and available image data to reproduce (some of) the experiments of these publications. Interested participants can make this demonstration a part of their presentation.

Announcements

  • [07.04.2014] The first meeting in on April 9th in 01.16.020.
  • [29.01.2014] If you missed the intro meeting and are still interested in participating, please see the intro slides and drop me a note via email.
  • [23.01.2014] There will be a short preliminary meeting on Wednesday January 29th, 2014 at 14h in 03.13.010. The list of papers will be made available after the introduction meeting in April.

Regulations

In this Master Seminar (formerly Hauptseminar), each student is asked to select one paper from a list. In order to successfully complete the seminar, participants have to fulfill these requirements:

  • Presentation: The selected paper is presented to the other participants (20 minutes presentation 10 minutes questions). Use the CAMP templates for PowerPoint CAMPmaster.pot, or Latex: CAMP-latex-template.zip.
  • Written Handout: A document of 4-8 pages is written and sent two days before the presentation to Fausto Milletari (i.e., on the Monday morning before the final presentation). Please download and use the llncs2e.zip Latex template. It can be edited and updated following comments in the final presentation.
  • Attendance: Participants have to participate actively in all seminar sessions.

Each presentation is followed by a discussion and everyone is encouraged to actively participate. The handout must include all references used and should be your own review of the paper (don't copy & paste). Both handout and presentation will have to be in English. It can follow the structure of the presentation: Intro (incl. statement of the problem, prior work, contribution of the present work), Methods (previously existing and improvements), Experiments (data and results), Conclusion / Summary.

Schedule

The seminar consists of a preliminary meeting, an introductory meeting and seminar sessions. Each of the sessions will consist of several student presentations. All seminar participants are expected to be present at every session and to actively participate in the discussion.

Date Time Location By Supervision Type Of Presentation Materials
Jan 29 14:00-15.00   - - Preliminary Meeting -
Apr 9 10.00-12:00 !!01.16.020!! - - First Meeting -
Apr 23 10.00-12:00 03.13.010 Graumann, Weiss, Bork Menze, Cobzas, Menze Rehearsal -
Apr 30 10.00-12:00 03.13.010 Gbakinro, Lee, Declara Golkov, Golkov, Cobzas Rehearsal -
May 7 10.00-12:00 !!01.16.020!! - - Rehearsal -
May 14 10.00-12:00 03.13.010 Mashood, El-Fiky, Fernando Shi, Menze, Cobzas, Rehearsal -
May 21 10.00-12:00 03.13.010 Nejatbakhsh, Raymond, Swami Shi, Shi, Menze Rehearsal -
May 28 10.00-12:00 03.09.12 Fernando, Declara, Weiss Cobzas, Cobzas, Cobzas !!! Final !!! -
Jun 4 10.00-12:00 03.13.010 Sarhan, Davoudi, Gomez Menze, Menze, Golkov Rehearsal -
Jun 11 10.00-12:00 03.13.010 Bork, Graumann, Swami Menze, Menze, Menze Final -
Jun 18 10.00-12:00 03.13.010 Lee, Gomez, Gbakinro Golkov, Golkov, Golkov Final -
Jun 25 10.00-12:00 03.13.010 Mashood, Nejatbakhsh, Raymond Shi, Shi, Shi Final -
Jul 2 10.00-12:00 03.13.010 El-Fiky, Davoudi, Sarhan Menze, Menze, Menze Final -
Jul 9 10.00-12:00 03.13.010 - - Final -


List of Papers

The papers that we are going to discuss in the seminar belong to four different research areas:
Area Description
Spatial Maps and Structures Spatial atlases and parametric maps that encode the variation of anatomy throughout the population in a probabilistic fashion.
Time series & signal models Dynamical models that describe blood flow patterns in MR and CT, or the dynamics of metabolic pathways as measured via PET, or the signals of short term water diffusion.
Spatio-temporal processes & signals Spatio-temporal models that describe spatially coupled time signal models, tumor growth, model personalisation.
Global processes Global probabilistic models that relate image features with global clinical information or global genetic variables.


In order to express your preferences about the topic you would like to discuss in your presentation and essay, please send an email to img.based.biomedical.modeling@gmail.com indicating the two papers your are most interested in. We will discuss the assignments in the meeting on April 9th.

Date Student Tutor Area Author Papers
  Bork Menze Spatial Maps and Structures Van Leemput et al.  PDF Automated model-based tissue classification of MR images of the brain. TMI 1999.
 CODE
  (available) Cobzas/Menze Spatial Maps and Structures Sabuncu et al.  PDF A generative model for image segmentation based on label fusion. TMI 2010.
 CODE
  Graumann Menze Spatial Maps and Structures Iglesias et al.  PDF Robust brain extraction across datasets and comparison with publicly available methods. TMI 2011.
 CODE
  (available) Menze Spatial Maps and Structures Tustison et al.  
  (available) Cobzas/Menze Spatial Maps and Structures Riklin-Raviv at al.  PDF Segmentation of image ensembles via latent atlases. Medical Image Analysis 2010.
MATLAB CODE AVAILABLE
  Declara Cobzas Spatial Maps and Structures Wang et al.  PDF Multi-atlas segmentation without registration: a supervoxel-based approach. Proc MICCAI 2013.
  (available) Cobzas Spatial Maps and Structures Wu et al.  PDF Minimizing joint risk of mislabeling for iterative patch-based label fusion. Proc MICCAI 2013.
  Weiss Cobzas Spatial Maps and Structures Chung et al.  PDF General multivariate linear modeling of surface shapes using SurfStat?. NeuroImage? 2010.
 CODE
           
  Mashood Shi Time series & signal models Gunn et al.  PDF Positron emission tomography compartmental models. Journal of Cerebral Blood Flow and Metabolism 2001.
CODE AVAILABLE
  Nejatbakhsh Shi Time series & signal models Kelly et Brady.  PDF A model to simulate tumour oxygenation and dynamic [18F]-Fmiso PET data. Phys Med Biol 2006.
CODE AVAILABLE
  (available) Menze Time series & signal models Schmid et al.  PDFBayesian methods for pharmacokinetic models in dynamic contrast-Enhanced magnetic resonance imaging, TMI 2006
 CODE
  Lee Golkov Time series & signal models Lenglet et al.  PDFMathematical methods for diffusion MRI processing. NeuroImage? 2009.
  Gomez Golkov Time series & signal models Assemlal et al.  PDF Recent advances in diffusion MRI modeling: Angular and radial reconstruction. Medical Image Analysis 2011.
  Gbakinro Golkov Time series & signal models Jones et al.  PDF White matter integrity, fiber count, and other fallacies: The do's and don'ts of diffusion MRI. NeuroImage? 2013.
           
  (available) Kelm Spatio-temporal processes & signals Kelm et al.  PDF Using spatial prior knowledge in the spectral fitting of MRS images. NMR Biomedicine 2011
 CODE
  (available) Kelm Spatio-temporal processes & signals Kelm et al.  PDF Estimating kinetic parameter maps from dynamic contrast-enhanced MRI using spatial prior knowledge. TMI 2006
 CODE
  Raymond Shi Spatio-temporal processes & signals Huang et al.  PDF Learning brain connectivity of Alzheimer's disease by sparse inverse covariance estimation. Neuroimage 2010
CODE AVAILABLE
  El-Fiky Menze Spatio-temporal processes & signals Clatz et al.  PDF Realistic simulation of the 3-D growth of brain tumors in MR images coupling diffusion with biomechanical deformation. TMI 2005
  Davoudi Menze Spatio-temporal processes & signals Konukoglu et al  PDFImage guided personalization of reaction-diffusion type tumor growth models using modified anisotropic eikonal equations. TMI 2010
 CODE
           
  Sarhan Menze Global processes Sabuncu et Van Leemput.  PDF The relevance voxel machine: a self-tuning Bayesian model for informative image-based prediction. TMI 2012
 CODE
    Menze Global processes Fonteijn et al.  PDF An event-based model for disease progression and its application in familial Alzheimer's disease and Huntington's disease. Neuroimage 2012
  Fernando Cobzas Global processes Cardoso et al.  PDF Geodesic information flows. Proc MICCAI 2012.
 CODE
  Swami Menze Global processes Kandel et al.  PDF Predicting cognitive data from medical images using sparse linear regression. Proc IPMI 2013
 CODE


Literature and Helpful Links

A lot of scientific publications can be found online.

The following list may help you to find some further information on your particular topic:

Some publishers:

Libraries (online and offline):

Some further hints for working with references:

  • JabRef is a Java program for comfortable working with Bibtex literature databases. Handy feature: if you know the PubMed ID for an article, JabRef can import data from there (via "Web Search/Medline").
  • Mendeley is a cross-platform program for organising your references.

If you find useful resources that are not already listed here, please tell us, so we can add them for others. Thanks.


TeachingForm
Title: Image-based biomedical modeling
Professor: Prof. Bjoern Menze
Tutors:  
Type: Hauptseminar
Information: Hauptseminar, SWS: 2, ECTS: 4
Term: 2014SoSe
Abstract:  


Edit | Attach | Refresh | Diffs | More | Revision r1.23 - 13 Jul 2015 - 12:17 - BjoernMenze

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