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Structural Magnetic Resonance Image Analysis for Neuroscientists

Organized by Meritxell Bach Cuadra (MIAL) & Ferath Kherif (LREN)

1.5 ECTS


Magnetic Resonance Imaging (MRI) is today a key component in diagnosis and therapy planning in many medical areas such as neurology, oncology, surgery, etc. Every day MRI scanners generate an impressively increasing amount of data. In this context, image analysis becomes central to process and quantify in a precise and reproducible manner all these images. In this course we will introduce basic imaging processing methods to quantitatively analyze structural MR imaging. Our goal is to provide the students with the basic knowledge and practical experience in MR image registration, segmentation and morphometry analysis.

We encourage students that are curious to better understand the image processing methods behind widely used structural image analysis tools, like SPM, to participate to this course. This year, both theory and practice will be equally important. Students who took part on the same course last year can also participate.

DATES: Wednesdays, from 10h to 13h. February 6, 13, 20 and 27 / March 6 and 13, 2013 

LOCATION: CHUV, Room Micropolis, Rue du Bugnon 23, Lausanne.


  • Presentation of the course
    Basics of rigid image volume registration
    Practical session (MITK and rigid registration)
  • Basics of non-rigid image volume registration
    Practical session (MITK and SPM)
  • Anatomical atlases and template construction
    Tissue segmentation of healthy brain: SPM model
    Practical session
  • Voxel-based morphometry
    Practical session
  • Journal Club
    Invited talk
  • Journal Club
    Invited talk

EVALUATION: Article presentation & discussion. Participation to the lectures is mandatory.

REGISTRATION: Please register by e-mail to the LN Coordinator before January 15th 2013. Limited number of participants to 20.


Introduction to Matlab

Organized by Jean-François Knebel (FENL), Meritxell Bach-Cuadra (MIAL) and Marzia De Lucia (FENL)

1.5 ECTS


This course is an introduction to the elements and practicalities of computer programming through the MATLAB mathematical computing environment. No previous programming experience is required. At the end of the course students will have the basics for using MATLAB in their own project work.


The course is organized in four sessions, each of them include one hour of theory and two hours of hands-on exercises. The topics are organized as follows:

Session 1: Course description; User interface; Path directory and ‘Help’; Vectors and Matrices; Arithmetic operators and basic functions; Miscelaneous (case sensitive, displayed numbers); Examples of what Matlab can do for you.

Session2: Reminder of basic functions; Other more complex functions; Basic programming (if-else-end, for-end, while-end); User interaction (disp, input); Hands on session with exercises

Session 3: Structures & cells; Importing / exporting data (reading / writing text files, csv & xls files); Saving / loading data (MAT files); Hands on session with exercises; Define and analyze needs of your own project

Session 4: Students present the MATLAB projects they would like to implement for the final exam in the context of their research interests and needs.

Session 5: Plots; Scripting (use of comments %%) and M-files; Share of code and scripts in Mathworks; Hands on session with exercises; Start to develop your own project (1 hour)

Session 6: Develop your own project. This is a hands-on-session where students develop their matlab project with the help of the organizers.

Session 7: Exam session

LOCATION: The course will take place in the room Micropolis, Rue du Bugnon 23, Lausanne.

DATES: From 9h-12h, on 27 Sep 2012, 03 Oct 2012, 11 Oct 2012, 18 Oct 2012, 25 Oct 2012, 01 Nov 2012, 13 Dec 2012.

Participants will be requested to develop a short project using MATLAB, related to their own research activity. Evaluation criteria:

  • Clear and precise definition of the research context and goals of the project
  • Students should be able to run completely the program and discuss the results
  • Students must present their code and results in a presentation format and should be able to explain all steps of the code
  • Both presentation and code quality will be evaluated (code should be clear and commented)
  • The participation to Session 1 to 5 (included) is mandatory to be accepted for the exam Session.

By e-mail to the LN Coordinator before September 15th. Number of participants will be strictly limited to 20.
Final confirmation of admission will be sent as soon as possible by the organizers on a first-come first-served basis. 

CIBM - Signal Processing Core, CHUV Unit - BH 08 - Rue du Bugnon 46 - CH-1011 Lausanne
Tel. +41 21 314 67 75