Basic fMRI Analysis

Course goals

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

Content

Period (from – till): 3 February 2027 - 03 March 2027 (BMS_P2_A).

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

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. Basic understanding of analysis techniques is not only relevant for students who are planning to work with fMRI data, but also necessary for critical evaluation of existing literature.  The course will provide students with hands-on experience with the execution of the most well established techniques and perform a full fMRI analysis from individual datasets to groupwise results. Students will learn to perform the necessary steps using the SPM12 software package (Statistical Parametric Mapping 2012). The course includes:
-General properties of the MRI/fMRI data formats
-fMRI preprocessing including:

1. Correction for subject head motion in the scanner (realignment)
2. Aligning MRI images of different modalities (coregistration)
3. Accounting for differences in timing of the different slices in fMRI datasets (Slice timing correction)
4. Transforming individual brains to standard space to allow for comparisons across subjects (Normalization)

-Statistical Analysis including:

1. Detecting brain activity in individual subjects using the General Linear Model
2. Correcting the statistical results for multiple comparisons
3. Performing second-level/groupwise statistics using the General Linear Model

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 course is a prerequisite for following the Advanced fMRI analysis course.
 
Literature/study material used:
-SPM12 starters Guide
-SPM12 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:
Basic Statistical Knowledge