Turku PET Centre Brain Imaging Course 2024

Principles And Applications of Neuroimaging Data Analysis

September 2024

This page contains preliminary information for the course, details will be updated as soon as possible

Turku PET Centre neuroscientists and Human Emotion Systems Laboratory are happy to announce that the fourth edition of our popular PET-MRI neuroimaging course will be held in September 2024. This one-week course will provide an 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. Masters’ students are also welcome. The course is free and open for everyone but registration is mandatory (see below).

Participants are assumed to have rudimentary knowledge of human brain anatomy and function, neuroimaging, as well as basics of relevant mathematics and physics. After the course, the participants should know the basics of analysing 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 adapted to any analysis platform.

Registering and ECTS credits

The course is arranged as a part of the curriculum for master’s degree in Psychology at the University of Turku with course code PSYK8965 and University of Turku students should register through the Peppi system. External students should register through the link below.

Completing the lectures + demonstrations + examination totals 5 ECTS for our own MA / PhD students. If you are not studying at University of Turku, we can however give (on request) a certificate of participation stating that attending the lectures and the remote computer lab sessions for the course cover approximately 3 ECTS credits. Unfortunately examination cannot be arranged online for external students. Please contact ms. Minna Kangasperko at PET Centre office or details.

Registration has not yet been opened. Check back later.

Lectures

All lectures will be held on site in University of Turku in lecture hall Pub4 in Public building. Lectures will also be streamed using Echo360 platform. It is recommended that you use a desktop computer or laptop (rather than tablet computer) for viewing the lectures so you too can follow the online and hands-on demonstrations. Lecture duration is ~45 minutes +10 minutes for questions. When logging on to Echo360, select the the currently active class to view the live stream. You need to manually advance to the next class when the previous one ends. Lectures will be stored permanently and they can also be viewed afterwards, the recordings are available almost immediately after the live stream ends.

Link to Echo360 will be posted here when the course begins.

Computer lab exercises

We will also arrange 6 computer lab exercise sessions. Computer labs will be held in University of Turku computer labs Due to space constraints in the computer lab, we will unfortunately have to limit on-site attendance. Priority is given to 1) University of Turku Master’s students for whom the course is a compulsory part of the curriculum and 2) University of Turku Psychology program students / Turku PET Centre staff and faculty. Possible extra seats will be assigned on first-come-first-served basis. We will however stream the lab sessions, make data, code and exercises available and arrange the labs so that you can follow them using your own workstation as long as you install the required software and datasets (see below) before the sessions. The computer lab server is only accessible with University of Turku account but anyone can follow the demonstrations. For UTU users make sure you have your UNIX permissions set up at http://idm.utu.fi/

Link to Echo360 will be posted here when the course begins.

Asking questions remotely

Echo360 discussion forum does not work without local account thus we have set up a Discord channel for questions & answers. Because the lectures will be recorded, the speakers will discuss the questions and comments after rather than during each lecture. Our team will follow the channel constantly and we will do our best to answer all the either immediately or after the lectures.

Link to Discord will be posted here when the course begins.

Schedule

The schedule below is in Helsinki time (EEST), which is UTC+3. Changes are still possible so please re-check the schedule on the webpage and on Echo360 before the course starts. Slides to the lectures (PDF) will be provided on this page, use the link above for accessing the recorded lectures.

Lectures day 1: Principles of brain imaging

8:30-9:15 Introduction: Basic principles of human neuroimaging (Lauri Nummenmaa)
9:15-10:00 Basics of biological modelling with PET data (Riku Klén)
10:00-10:45 Principles of pharmakokinetic modelling (Jussi Hirvonen)
10:45-12:00 Lunch break
12:00-12:45 Brain-PET modelling in clinical studies (Marco Bucci)
12:45-13:30 Preprocessing volumometric brain imaging data (Jouni Tuisku)
13:30-13:45 Coffee break (with pulla!)
13:45-14:30 Using Carimas software for image analysis (Chunlei Han)
14:30-15:15 Practical framework for brain-PET data modelling (Jouni Tuisku)
15:15-16:00 Population level inference with neuroimaging data (Lauri Nummenmaa)

Lectures day 2 : Practical issues in brain imaging and analysis

8:30-9:15 Physiology of the BOLD signal (Kerttu Seppälä)
9:15-10:00 Experimental designs for fMRI (Lauri Nummenmaa)
10:00-10:45 Practical framework for preprocessing fMRI data (Vesa Putkinen)
10:45-12:00 Lunch break
12:00-12:45 General Linear Model for fMRI analysis (Kerttu Seppälä)
12:45-13:30 First level models for fMRI (Lihua Sun)
13:30-13:45 Coffee break (with pulla!)
13:45-14:30 Second level models for fMRI (Severi Santavirta)
14:30-15:15 Region of interest analysis for PET and MRI (Lauri Nummenmaa)
15:15-16:00 Neuroimaging data visualization (Vesa Putkinen)

Lectures day 3: Advanced topics in brain signal analysis

8:30-9:15 Linear mixed models in neuroimaging (Tuulia Malen)
9:15-10:00 Statistical Pattern Recognition with fMRI (Heini Saarimäki)
10:00-10:45 Imaging whole-body biological circuits with total-body PET (Lauri Nummenmaa)
10:45-12:00 Lunch break
12:00-12:45 Model-free analysis of BOLD-fMRI data (Severi Santavirta)
12:45-13:30 Neuroinformatics and large-scale analysis (Lauri Nummenmaa)
13:30-14:00 Wrap-up with coffee and pulla (All speakers)

Virtual lecture by Mr Yngwie Malmsteen can be viewed here

Computer labs day 4: Data preprocessing

8:30-10:45 Working with 3D brain data and learning the basic tools (TBA)
11:30-13:45 Segmenting, warping and coregistering 3D brain data
14:00-16:15 Pharmacokinetic modelling and preprocessing of brain-PET data (TBA)

Computer labs day 5: Statistical inference from brain imaging data

8:30-10:45 Preprocessing functional MRI data (TBA)
11:30-13:45 Statistical modelling of functional MRI data (TBA)
14:00-16:15 Population level inference and visualisation (TBA)

Resources used on the computer lab sessions

For those attending the computer labs locally, all necessary software will be installed on a virtual server. We will stream the lab sessions, make data, code and exercises available and arrange the labs so that you can follow them using your own workstation as long as you install the required software and datasets (see below) before the sessions. Unfortunately we cannot provide technical support for the installation process. Please make you have access to the following tools and dependencies to participate:

Matlab: Industry standard programming and numeric computing platform
SPM12: Multimodal (MRI / PET / EEG / MEG) data processing and analysis suite, runs on Matlab
Surf Ice: fast and efficient surface rendering tool, highly recommended if you want to work using GUI
MRIcroGL: Graphially more advanced and faster version of old MRIcron with better 3D handling capabilities
MAGIA: Comprehensive PET modelling & preprocessing suite
fMRIPrep
: Robust fMRI preprocessing suite

PET dataset 1

This is the full NRM dataset with the LondonPride ligand, kindly provided by the King’s College London PET team. The dataset consists of two PET scans (and associated files) per subject: a baseline scan and a displacement scan. The dataset is available from NITRC via this link.

PET dataset 2

This is a subset of the LondonPride dataset that is used in the computer lab sessions for learning MAGIA, the in-house data processing pipeline hosted by Turku PET Centre. Use link1, and link2 to download the data.

MRI dataset

This small dataset from Turku PET Centre contains EPI and T1 data from an experiment, where the subjects viewed pictures with varying content. The dataset is available via these links: link, link2.

Lab session exercises and notes

The lab session exercises and notes contain all the assignments that will be used on the computer classes. Please download the package and the data above if you wish to work through the assignment at your own pace. Link will be updated before the course starts.

Previous editions of the course

Turku PET Centre Brain Imaging Course 2023 edition can be found here
Turku PET Centre Brain Imaging Course 2022 edition can be found here
Turku PET Centre Brain imaging course 2021 edition can be found here
Turku PET Centre Brain imaging course 2017 edition can be found here