Turku PET Centre Brain Imaging Course 2021

Principles And Applications of Neuroimaging Data Analysis

Turku PET Centre neuroscientists are happy to announce that the second edition of our PET-MRI neuroimaging course will be held on August 18.-20. 2021. This course will give a hands-on overview on the basic brain imaging analysis techniques applicable to PET as well as structural and functional MRI data. The course is aimed at PhD students, post-docs, and scientists working on medical, cognitive, and computational neuroimaging. Participants are assumed to have rudimentary knowledge of neuroimaging and working with PET and MRI data, but this is not strictly necessary. After the course, the participants should be able to independently process and analyse the data that has been retrieved from PET camera / MRI scanner. Analytic pipeline will focus on the PET Centre brain data analysis framework but can be adopted to any analysis platform.


The course is free and not restricted to University of Turku staff and students, but registration is mandatory. We can accommodate a maximum of 120 participants locally so bookings will be done on first-come-first-served basis. The lectures will be available live on Zoom. Remote viewing has no seat limit but you will still need to register to get access. To register for the course, please email Turku PET Centre secretary Ms. Lenita Saloranta (lensal@utu.fi) stating your name and study program or research group. Write “Brain-PET registration” to the subject field of your email.

Practical information

The lectures will be held in Pub2 lecture room in Publicum, Assistentinkatu 7. It is strongly recommended that you bring your own laptop with you to the course so you can follow the online and hands-on demonstrations.

The course is arranged outside the formal University of Turku degree system so we cannot give study credits directly for the participation. We will however give certificate of participation stating that the course covers approximately 2 ECTS credits.

Pleaser contract prof. Lauri Nummenmaa for details. See you in Turku in August!


Wednesday August 18th: Principles of brain imaging

8:00-9:00 Basic principles of human neuroimaging (Lauri Nummenmaa)
9:00-9:45 Preprocessing volumometric brain imaging data (Jouni Tuisku)
9:45-10:00 Coffee break
10:00-11:00 Analyzing Diffusion Tensor Imaging data (Virva Saunavaara)
11:00-12:00 Pharmakokinetic modelling of PET data: Principles (Jussi Hirvonen)
12:00-13:00 Lunch break
13:00-14:00 Pharmakokinetic modelling of PET data: Applications with MAGIA pipeline (Jouni Tuisku)
14:00-15:00 Using Carimas software for image analysis (Chunlei Han)
14:45-15:00 Coffee break
15:00-16:00 Second level analysis of PET data (TBA)

Thursday August 19th: Basics of fMRI analysis

8:00-9:00 Physiology of the BOLD signal and image acquisition (Kerttu Seppälä)
9:00-9:45 GLM for fMRI analysis (Kerttu Seppälä)
9:45-10:00 Coffee break
10:00-11:00 Experimental designs for fMRI (Lauri Nummenmaa)
11:00-12:00 Preprocessing with fMRIprep (Vesa Putkinen)
12:00-13:00 Lunch break
13:00-14:00 First level models (Lihua Sun)
14:00-15:00 Second level models (Severi Santavirta)
14:45-15:00 Coffee break
15:00-16:00 Data visualization (Vesa Putkinen)

Friday August 20th: Advanced topics in brain signal analysis

8:00-9:00 Bayesian approach for regional modelling (Tuulia Malen)
9:00-9:45 Statistical Pattern Recognition with fMRI (Heini Saarimäki)
9:45-10:00 Coffee break
10:00-11:00 Connectivity analysis (TBA)
11:00-12:00 Model-free analysis of BOLD-fMRI data (Severi Santavirta)
12:00-13:00 Lunch break
13:00-13:45 Neuroinformatics and large-scale analysis (Lauri Nummenmaa)
13:45-14:00 Coffee break
15:00-16:00 Wrap-up (All speakers)

Virtual lecture by Mr Malmsteen can be viewed here


MAGIA toolbox

MAGIA is a comprehensive brain-PET modelling suite, which has been optimised for large-scale brain-PET analysis. MAGIA is installed on the Yngwie neuroimaging server and thus available to PET Centre neuroscientists. If you want to install magia on your own computing framework, you can download the source from our git repository.

Data analysis software and tools

SPM12: Multimodal (MRI / PET / EEG / MEG) data processing and analysis suite, runs on Matlab
FSL: Standalone MRI data processing and analysis suite
Freesurfer: Standalone tool for analysis and visualization of structural and functional neuroimaging. Most well known for the excellent cortical surface mesh generation algorithms
AFNI: Standalone MRI data processing and analysis suite
BrainVoyager: Standalone commercial MRI data processing and analysis suite
PMOD: Standalone commerical PET modelling and image processing tool

DTI tools

DTIprep: General-purpose too for DTI analysis
FSL: has also good tensor fitting packages as well as tools for tract-based analysis
ExploreDTI: a graphical toolbox for tractography

Volumometric image viewer tools

MRIcron: Image viewer with basic analytic, image manipulation and ROI drawing capabilities
Mango: Advanced volumometric viewer with image editing and rendering capabilities (http://ric.uthscsa.edu/mango/)
Carimas: Medical image analysis platform developed at Turku PET Centre.  Capable of visualization, segmentation and modelling of multiple types of medical images
Freeview: Built-in viewer for Fressurfer. Excellent for viewing 2D and 3D images in tandem
FSLview: Built-in image viewer for FSL. Good capailities for volume viewing

3D rendering tools

Freeview: Built-in viewer for Fressurfer. Excellent for viewing 2D and 3D images in tandem
3dSlicer: Open-source software package for visualization and medical image computing
Caret: Multi-purpose surface visualization and analysis tool
MRIcroGL: Graphially more advanced and faster version of MRIcron with better 3D habdling capabilities
FSLview can also do some 3D image rendering