Hauptseminar: Advances in Spatio-Temporal Medical Image Processing: Theory and Applications

Nassir Navab, Abouzar Eslami, Mehmet Yigitsoy, Kristof Ralovich

Type: Advanced Seminar Course Module IN8901
Type: Master Seminar Module IN2107
Type: Seminar Module IN0014
SWS: 2+0
ECTS: 4 Credits
Course Language: English
TUM-Online: Advances in Spatio-Temporal Medical Image Processing: Theory and Applications

Announcements

• The first meeting will be on Oct. 27 at 10:30 in our seminar room (MI 03.13.010).

Requirements

In this Master Seminar (formerly Hauptseminar), each student is asked to select one topic from the list below. 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.
• Written Handout: A document of maximum 8 two-column pages in IEEE format is written and submitted one week after the 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 must be written completely in your own words. Copy and paste wont be tolerated. Both handout and presentation have to be done in English.

Registration

Interested students, please take a look at the papers listed below and select one you would like to base your seminar talk on. Registration is done via TUM-Online. Then please send an email to Mehmet Yigitsoy (), including your paper choice, your name, your birthday, program of study and Matrikelnummer.

Schedule

We will have an introduction to the seminar course in the first session. Students are expected to pick their topics by the second session.

• Thu, 27.10.2011, 10:30 - 12:00
• Thu, 03.11.2011, 10:30 - 12:00

Reserved time slots for students presentation:

• Thu, 22.12.2011, 10:30 - 12:00
• Thu, 12.01.2012, 10:30 - 12:00
• Thu, 19.01.2012, 10:30 - 12:00
• Thu, 26.01.2012, 10:30 - 12:00
• Thu, 02.02.2012, 10:30 - 12:00

We expect to finish earlier than listed here. The final schedule of presentations depend on the number of students and distribution of talks.

Topics

Please choose one of the following papers for your seminar presentation. For obtaining the full-text PDFs, please use Google and especially Google Scholar. In case you are interested in a paper but cannot find the full text, please contact your course supervisor.

Spatio-temporal Registration, Motion Estimation

• Glocker, Sotiras et al.: Deformable Medical Image Registration: Setting the State of the Art with Discrete Methods, Annu Rev Biomed Eng (2011)
• Vandemeulebroucke and Rit et al.: Spatiotemporal motion estimation for respiratory-correlated imaging of the lungs, Medical Physics (2011)
• Ehrhardt, Werner et al.: Statistical Modeling of 4D Respiratory Lung Motion Using Diffeomorphic Image Registration, IEEE-TMI (2010)
• Schmidt-Richberg, Werner et al.: Estimation of Slipping Organ Motion by Registration with Direction-Dependent Regularization, MIA (2011)
• Zhang, Brady et al.: Spatio-temporal (2D+ T) non-rigid registration of real-time 3D echocardiography and cardiovascular MR image sequences, PMB (2011)
• Serag, Aljabar et al.: Construction of a 4D atlas of the developing brain using non-rigid registration, ISBI (2011)
• Lorenzi, Ayache et al.: Schild’s Ladder for the Parallel Transport of Deformations in Time Series of Images, IPMI (2011)
• Sofka and Stewart: Location registration and recognition (LRR) for serial analysis of nodules in lung CT scans, MIA (2010)
• Chun, Shretter et al.: Sufficient condition for local invertibility of spatio-temporal 4D B-spline deformations, ISBI (2010)
• Han, Bayouth et al.: Characterization and identification of spatial artifacts during 4D-CT imaging, Medical Physics (2011)

Cardiac Image Analysis

• Lombaert et al.: Statistical Analysis of the Human Cardiac Fiber Architecture from DT-MRI, FIMH (2011)
• Linte et al.: Targeting Accuracy under Model-to-Subject Misalignments in Model-Guided Cardiac Surgery, MICCAI (2009)
• Pauly et al.: A Machine Learning Approach for Deformable Guide-Wire Tracking in Fluoroscopic Sequences, MICCAI (2010)
• Petitjean and Dacher: A review of segmentation methods in short axis cardiac MR images, MedIA^?(2011)
• Schaerer et al.: A dynamic elastic model for segmentation and tracking of the heart in MR image sequences, MedIA^? (2010)
• King et al.: Respiratory motion correction for image-guided cardiac interventions using 3-D echocardiography, MedIA^?(2010)
• Duchateau et al: A spatiotemporal statistical atlas of motion for the quantification of abnormal myocardial tissue velocities , MedIA^?(2011)
• Huang et al.: Dynamic 2D Ultrasound and 3D CT Image Registration of the Beating Heart, IEEE TMI (2009)
• Wilson et al.: Mapping of Cardiac Electrophysiology Onto a Dynamic Patient-Specific Heart Model, IEEE TMI (2009)
• Suinesiaputra et al.: Automated Detection of Regional Wall Motion Abnormalities Based on a Statistical Model Applied to Multislice Short-Axis Cardiac MR Images, IEEE TMI (2009)
• Wein et al.: Towards Guidance of Electrophysiological Procedures with Real-Time 3D Intracardiac Echocardiography Fusion to C-arm CT, MICCAI (2009)
• Mingxing et al.: Non-rigid Reconstruction of the Beating Heart Surface for Minimally Invasive Cardiac Surgery, MICCAI (2009)
• Zhang et al.: Congenital aortic disease: 4D magnetic resonance segmentation and quantitative analysis, MedIA^?(2009)
• Sermesant et al.: Patient-specific electromechanical models of the heart for the prediction of pacing acute effects in CRT: A preliminary clinical validation, MedIA^? (2011)
• Liu and Prince: Shortest Path Refinement for Motion Estimation From Tagged MR Images, IEEE TMI (2010)
• Yang et al: Predication Based Collaborative Trackers (PCT): A Robust and Accurate Approach Toward 3D Medical Object Tracking, TMI (2011)
• Zheng et al: Four-chamber heart modeling and automatic segmentation for 3-D cardiac CT volumes using marginal space learning and steerable features. IEEE TMI (2008)
• Zhang et al: 4-D cardiac MR image analysis: left and right ventricular morphology and function. IEEE TMI (2010)

Aortic Blood Flow Simulation

• Friman et al: Probabilistic 4D Blood Flow Tracking and Uncertainty Estimation, MedIA^? (2011)
• Xiong et al: Physics-based modeling of aortic wall motion from ECG-gated 4D computed tomography, MICCAI (2010)
• Coogan et al: Computational Fluid Dynamic Simulations of Aortic Coarctation Comparing the Effects of Surgical- and Stent-Based Treatments on Aortic Compliance and Vent ricular Workload, Catheterization and Cardiovascular Interventions (2011)
• Kim et al: On Coupling a Lumped Parameter Heart Model and a Three-Dimensional Finite Element Aorta Model, Ann. Biomed. Eng.(2009)

Essay/Talk

Presentation (about 30-45min) followed by a discussion. Essay (10 pages) including all references used. The essay and presentation have to be done in English for Hauptseminars and German or English for Proseminars. The essay must be written in your own words and not by copy and paste.

For Windows users:

• install miktex - TeX implementation for Microsoft Windows
• install TeXnicCenter - integrated development environment (IDE) for developing LaTeX-documents on Microsoft Windows
• Use the The Not So Short Introduction to LaTex to get started with LaTex.
• Use this latex template for the essay.

Your talk:

• Please use this PPT template.
• How to Present a Paper in Theoretical Computer Science: A Speaker's Guide for Students by Ian Parberry
• The outline should be sent to the supervisor four weeks before the presentation.
• The presentation slides and essay should be finalized and discussed with the supervisor one week before the presentation.
• The essay is due at the day of the last presentation of the seminar.

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.