Lecture: Image Acquisition and Analysis in Neuroscience

Course

  • Lecturer(s):
  • Start: 23.10.2013, 10:30 am, LBH III.03a
  • Dates: Wed. 10:30 - 12 and Fri. 11 - 12:30
  • Course number: MA-INF 2312
  • Curriculum: Master , B-IT Master Life Science Informatics
  • Effort: 4.0 SWS

Exercises

Description

This page is outdated. Please find the 2015 class here.

Image-based methods in general and Magnetic Resonance Imaging in particular have become important tools in neuroscience: Imaging the living brain allows us to detect brain regions that engage in specific tasks, to investigate the wiring of the brain, to study and to recognize the effects of aging or disease. Recently, some image-based studies have even made the headlines, suggesting that MR imaging might be used to detect lies, diagnose psychiatric disease, or identify images viewed by the subject in the scanner.

This lecture will make you understand the computer science behind such results. In particular, image acquisition and analysis in neuroscience require the following computational methods:

  • Image reconstruction for Magnetic Resonance Imaging
  • (Multimodal) image registration
  • Building anatomical atlases
  • 3D Image Segmentation
  • Models for functional MRI (fMRI) and diffusion MRI (dMRI) data
  • Statistical Modeling
  • Machine Learning Approaches 

The lecture conveys an understanding of all these topics, and is ideally suited to prepare you for a lab course or a master thesis in this field. At the same time, you will learn about some fundamental methods in 3D image processing, statistical modeling, and machine learning, which are useful beyond their applications in neuroscience.

Organization

The lecture takes place twice a week - Wednesday and Friday - with an exercise class replacing the lecture on Friday roughly every other week. Lectures on image formation and reconstruction in Magnetic Resonance Imaging will be given by externDr. Tony Stöcker from the externDZNE. There will be individual oral exams at the end of the semester.

Slides

Assignment Sheets

Exercise 1: Fourier Transform
Assignment sheet  (PDF document, 386 KB)
Exercise 2: Registration
Assignment sheet  (PDF document, 177 KB)
Exercise 3: MRI
Assignment sheet  (PDF document, 303 KB)
Exercise 4: Segmentation
Assignment sheet  (PDF document, 197 KB)
Exercise 5: Statistical Testing
Assignment sheet  (PDF document, 173 KB)
Exercise 6: Diffusion MRI
Assignment sheet  (PDF document, 284 KB)