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
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.
Global processes	Global probabilistic models that relate image features with global clinical information or global genetic variables.
Spatial Maps and Structures	Spatial atlases and parametric maps that encode the variation of anatomy throughout the population in a probabilistic fashion.
Spatio-temporal processes & signals	Spatio-temporal models that describe spatially coupled time signal models, tumor growth, model personalisation.

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:

• Microsoft Academic Search
• Google Scholar
• CiteSeer
• CiteULike
• Collection of Computer Science Bibliographies

Some publishers:

• ScienceDirect (Elsevier Journals)
• IEEE Journals
• ACM Digital Library

Libraries (online and offline):

• http://rzblx1.uni-regensburg.de/ezeit/ (Elektronische Zeitschriften Bibliothek)
• Verbundkatalog des Bibliotheksverbundes Bayern (BVB)
• Computer ORG
• http://www.ub.tum.de/ (TUM Library)
  • To get access onto the electronic library, see http://www.ub.tum.de/medien/ejournals/readme.html
  • "proxy.biblio.tu-muenchen.de" mit Port 8080 (nur fuer http). Damit klappen zumindest portal.acm.org und computer.org meistens
• Various proceedings of conferences in our AR-Lab, 03.13.036 (These proceedings are not for lending!)

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.