Advanced fMRI Analysis

Course goals

At the end of the course the student has:
Familiarity with the basic fMRI processing and analysis techniques at the theoretical and practical level.

Content

Period (from – till): 17 March 2027 - 21 Apr 2027 (BMS_P3_A).

Course coordinator: Dr. Mathijs Raemaekers
E-mail: m.raemaekers-2@umcutrecht.nl 
Brain Center Rudolf Magnus
University Medical Center Utrecht

Faculty
Dora Hermes
Mathijs Raemaekers

Course description
Functional Magnetic Resonance Imaging (fMRI) is one of the major methods for measuring neural activity in humans, and techniques for processing and analysing the data are under constant development. Since the introduction of fMRI and its basic task based analysis, many additional processing and analysis techniques have been developed that shed a more elaborate light on the functioning of the human brain. Understanding and the ability to apply these techniques is a necessary requirement for current researchers in the fMRI research field. The course will provide students with hands-on experience on several modern techniques using various software packages. In addition, we will provide tools that can help students to further expand their knowledge and abilities, and also to evaluate the scientific merit of novel approaches regarding e.g. validity and replicability.
 
The course includes:

• Data driven analysis of fMRI data using Independent Component Analysis (ICA)
• Making and transforming 3D brain models e.g. for flatmapping and performing surface based analysis
• Classifying brain states using MultiVoxel Pattern Analysis (MVPA)
• Seed based analyses of brain connectivity
• Analysing Parametric modulations

There is a strong focus on practical application, where a theoretical background is immediately followed by implementation during combined lecture/workgroup sessions. In addition, students get home assignments to analyse data individually. The student must have a laptop with an installation of MATLAB 2007a or later. MATLAB with a student’s license can be obtained from https://students.uu.nl/gratis-software. All other software will be provided during the course. Following the Basic fMRI Analysis (BMB509117) course is a prerequisite for following the Advanced fMRI analysis course.
 

Assessment	Description	Weighing
DEELNAME	Active participation	20
OPDRACHT	Assignment	80

 
Literature/study material used:
-SPM12 starters Guide
-SPM12 manual
-GIFT Manual
-CARET Manual
-Reader fMRI preprocessing & analysis
-Lecture slides
Course material will be provided as PDF’s before and during the course.

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Students' site. Maximum participants 24.

Mandatory for students in Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes.

Prerequisite knowledge:
Having followed Basic fMRI analysis (BMB509117)