Turku PET Centre Neuroimaging Course 2022

Principles And Applications of Neuroimaging Data Analysis

Turku PET Centre neuroscientists and Human Emotion Systems Laboratory are happy to announce that the third edition of our PET-MRI neuroimaging course will be held on September 19th -21st 2022. 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. Masters’ students are also welcome. Participants are assumed to have rudimentary knowledge of human brain anatomy and function, 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 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 completing the lectures and examination totals 5 ECTS for our own MA / PhD students. If you are not studying at University of Turku, we can however give certificate (on request) of participation stating that the attending the lectures on the course cover approximately 2 ECTS credits. Please contact prof. Lauri Nummenmaa for details.

University of Turku master’s / PhD students can register for the course using the Peppi system starting August 2022. For external attendants please fill in this registration form.

Practical information

All lectures will be held on site in University of Turku lecture hall PUB2 (Publicum building). Lectures will also be streamed live using Echo360 platform. It is recommended that you use a desktop computer or laptop (rather than tablet computer) for viewing the lectures so you to 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 the Echo350 system will be posted here before the course starts

Asking questions remotely

Echo360 discussion forum does not work for those who do not have an account at our university 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 the Discord channel will be posted here before the course starts

Preliminary 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.

Monday September 19th: Principles of brain imaging

8:30-9:15 Introduction: Basic principles of human neuroimaging (Lauri Nummenmaa)
9:15-10:00 Crash course in nuclear medicine imaging (Kyoungjune “Arto” Pak)
10:00-10:45 Principles of pharmakokinetic modelling (Jussi Hirvonen)
10:45-12:00 Lunch break
12:00-12:45 From photons to images: Brain-PET modelling in action (TBA)
12:45-13:30 PET data modelling with MAGIA pipeline (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 Preprocessing volumometric brain imaging data (Jouni Tuisku)
15:15-16:00 Second level analysis of PET (and VBM) data (Lauri Nummenmaa)

Tuesday September 20th: Practical issues in brain imaging and analysis

8:30-9:15 Physiology of the BOLD signal and T*2 image acquisition (Kerttu Seppälä)
9:15-10:00 Experimental designs for fMRI (Lauri Nummenmaa)
10:00-10:45 Preprocessing fMRI data with fMRIprep (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 (TBA)
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 (TBA)
15:15-16:00 Effective neuroimaging data visualization (Vesa Putkinen)

Wednesday September 21st: Advanced topics in brain signal analysis

8:30-9:15 Bayesian statistical inference in neuroimaging (Tuulia Malen)
9:15-10:00 Statistical Pattern Recognition with fMRI (Heini Saarimäki)
10:00-10:45 Connectivity analysis (TBA)
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 Malmsteen can be viewed here

Data packages used in the course

PET dataset

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 for MAGIA

This is a subset of the LondonPride dataset for learning MAGIA, the in-house data processing pipeline hosted by Turku PET Centre. Download the dataset from this link.

fMRI dataset

This small dataset from Turku PET Centre contains EPI and T1 data from an experiment, where the subjects viewed pictures with varying content. Download dataset from this link.

LINKS TO SOFTWARE PAGES

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

Carimas: Medical image analysis platform developed at Turku PET Centre.  Capable of visualization, segmentation and modelling of multiple types of medical images.
MRIcron: Image viewer with basic analytic, image manipulation and ROI drawing capabilities, a reliable workhorse
Mango: Advanced volumometric viewer with image editing and rendering capabilities. A nice companion for mricron.
Freeview: Built-in viewer for Fressurfer. Excellent for viewing 2D and 3D images in tandem
FSLeyes: Built-in image viewer for FSL. Good capabilities for volume viewing and support for 4D visualisation.
FSLview: Previous version of FSLeyes.

3D rendering tools

Freeview: Built-in viewer for Freesurfer. Excellent for viewing 2D and 3D images in tandem
Surf Ice: fast and efficient surface rendering tool, highly recommended if you want to work using GUI
3dSlicer: Open-source software package for visualization and medical image computing
Caret: Multi-purpose surface visualization and analysis tool. No longer updated, integrated into connector workbench
MRIcroGL: Graphially more advanced and faster version of MRIcron with better 3D habdling capabilities
FSLview can also do some 3D image rendering

Previous editions of the course

Turku PET Centre Brain imaging course 2017 edition can be found here
Turku PET Centre Brain imaging course 2021 edition can be found here