Introduction to Neuroimaging Methods
Lectures and Workshops
Lectures and workshops will take place in January and February 2018 in the CBU West Wing Seminar Room (unless stated otherwise, please check below). They are structured in three blocks: MRI (Jan 1517), fMRI and Connectivity (Feb 1315), as well as EEG/MEG and Multimodal Imaging (Feb 1923). Workshops usually take about 2 hours, lectures may be shorter.
Details will be announced before individual events via this mailing list: http://lists.mrccbu.cam.ac.uk/mailman/listinfo/skillstraining (NonCBU people can subscribe by sending an email to skillstrainingsubscribe (at) mrccbu (dot) cam (dot) ac (dot) uk).
We expect attendees to have basic skills in scientific computing and programming, e.g. at the level taught in our previous workshops. It might help to refresh your memories a little bit.
Look here for other training opportunities in and around Cambridge.
Please contact OlafHauk with questions and feedback.

(f)MRI and Connectivity 



Jan 15 
Jan 16 
Jan 17 
Feb 13 
Feb 14 
Feb 15 
10:00:00 

MRI Physics I 
Introduction to Diffusion MRI 
fMRI Analysis I  preprocessing 
fMRI Analysis III  Group Statistics 
Graph Theory 
11:00:00 
Some Physics You Might Find Useful 








13:30:00 

MRI Physics II 
Lab tour and demo 
fMRI Analysis II  GLM 
fMRI/EEG/MEG Connectivity 

14:30:00 
EEG/MEG and Multimodal Imaging 


Feb 19 
Feb 20 
Feb 21 
Feb 22 
Feb 23 
10:00:00 
EEG/MEG 1  preprocessing 
EEG/MEG 2  Source Estimation 
Brain Stimulation 
EEG/MEG Analysis in SPM 
Source Estimation And Statistics in SPM 
11:00:00 







13:30:00 
MEG lab visit and demo 
EEG/MEG 3  timefrequency and functional connectivity 
Multimodal Imaging 

Multimodal Imaging In SPM 
14:30:00 
PREVIOUS schedule (with materials attached) 

April 26 
14.30 
Multivariate fMRI Analysis I PDF 
Marieke Mur 
Lecture + Workshop 
This workshop introduces linear classification, one of the most popular forms of multivoxel pattern analysis. We will give an overview of the most commonly used linear classifiers, and list the steps that are needed to implement a classification analysis. The workshop will include a handson matlab session, during which we'll go through example code that performs linear classification on an fMRI data set. 
May 3 
14.30 
Multivariate fMRI Analysis II PDF 
Marieke Mur 
Lecture + Workshop 
This workshop introduces representational similarity analysis (RSA), a more recent form of multivoxel pattern analysis which has gained popularity over the last few years. We will give an overview of the origin of RSA and how it relates to linear classification, and list the steps that are needed to implement RSA. The workshop will include a handson matlab session, during which we'll analyse the same fMRI data as last week, but this time using RSA. 
May 10 
14.00 
Rik Henson 
Lecture 
This lecture will describe possible generative models that can be used to integrate data from EEG, MEG and fMRI 

May 16 (Tuesday !!!) 
13.00 
Rik Henson 
Lecture 
This lecture will introduce concepts of functional and effective connectivity, briefly describe effective connectivity in fMRI (eg dynamic causal modelling) and then expand on the larger range of methods available for measuring connectivity with EEG/MEG. 

May 24 
14.30 
Diffusion MRI I 
Marta Correia 
Lecture + Workshop 
This workshop will cover the basic principles of diffusion MRI acquisition and data analysis. It will include a practical component covering preprocessing of diffusion MRI data, model fitting, group analysis of diffusion parameters and tractography. 
May 31 
14.30 
Diffusion MRI II 
Marta Correia 
Lecture + Workshop 
In this week’s workshop we will continue the hands on session for preprocessing of diffusion MRI data and introduce methods for group analyses. We will also cover more advanced diffusion MRI methods, including tractography and probabilistic modelling. 
July 26/27 

fMRI and EEG/MEG Analysis in SPM  from raw data to multimodal images 

WWSR 

Wed, July 26 
10.0012.00 
Introduction to EEG/MEG analysis in SPM 
Jason Taylor 
Lecture+Demo 
Introduction and overview of EEG/MEG analysis in SPM. 

14.0016.00 
fMRI analysis in SPM 
Jason Taylor & Rik Henson 
Lecture+Demo 
Demo of standard fMRI analysis in SPM12. 
Thu, July 27 
10.0012.00 
Source estimation and statistics in SPM 
Jason Taylor & Rik Henson 
Lecture+Demo 
Demo of source estimation and statistics in SPM12. 

14.0016.00 
Multimodal imaging workshop and Q&A 
Jason Taylor, Rik Henson, Hunar Abdulrahman 
Workshop 
Participants can analyse a multimodal data set under supervision, following chapter 42 of the SPM12 manual 
Previous Lent Term 

Date 
Time 
Title 
Presenter(s) 
Type 
Comments 
Jan 18 
14.30 
Olaf Hauk 
Lecture (~ 1h) 
Basic physical concepts needed for the interpretation of EEG/MEG and fMRI data. Electric potential, fields, atoms and spins... 

Jan 25 
14.30 
Marta Correia 
Lecture (~1.5h) 
This talk will cover the basic principles of MRI physics for beginners, including nuclear spins and net magnetization, excitation and relaxation mechanisms, slice selective gradients, frequency and phase encoding, image formation and kspace. 

Jan 30 (Monday!!) 
12.30 
Marta Correia 
Lecture 
This talk is aimed at fMRI beginners and will be divided into two parts. Firstly, I will talk about the biophysics of fMRI and the basic mechanism behind BOLD contrast. In the second half, I will discuss common image artefacts and ways to work around them. 

Feb 8 
14.30 
Johan Carlin 
Lecture + Workshop 
We will cover basic preprocessing of fMRI data, and some useful diagnostic visualisations to help spot problems. 

Feb 15 
14.30 
fMRI Analysis 2: Single subject analysis using GLM (workshop materials) 
Johan Carlin 
Lecture + Workshop 
This workshop covers the basic principles of singlesubject design focusing on how it is implemented in SPM. We will also discuss how to design efficient fMRI experiments. 
Feb 22 
14.30 
fMRI Analysis 3: Group analysis and statistical inference (workshop materials) 
Johan Carlin 
Lecture + Workshop 
After a short recap of the GLM, which also is the basis of group analysis, we will review some example designs. We will focus especially on statistical inference and multiple comparisons correction. 
Mar 1 
14.30 
Brain stimulation PDF 
Benedikt Zöfel 
Lecture (45 min approx.) 
This talk will provide an introduction to brain stimulation methods, with a focus on transcranial magnetic stimulation (TMS) and transcranial electrical stimulation (tES). I will cover the principles of these techniques, the physiological basis of the effects, the different protocols used, and examples of how brain stimulation can be used as an experimental and therapeutic tool. 
Mar 8 
14.30 
EEG/MEG 1: Preprocessing and Data Reviewing PDF 
Olaf Hauk 
Lecture + Workshop 
Signal generation, Maxfilter, Common artefacts, ICA, Averaging, MEGMRI Coregistration 
Mar 14 (!!!) Tuesday 
14.30 
EEG/MEG 2: Head Models and Source Estimation PDF 
Olaf Hauk 
Lecture+Workshop 
We will look at structural MRI data and reconstructed cortical surfaces, coregister MRI and MEG coordinate systems, talk about the basis theory of source estimation, and try some linear source estimation ourselves. We will then compare different methods as well as EEG and MEG with respect to spatial resolution using the concepts of pointspread and crosstalk. 
April 5 (postponed from March 22nd) 
14.30 
EEG/MEG 3: Timefrequency and Functional Connectivity Analysis PDF 
Olaf Hauk 
Lecture+Workshop 
Basics of Fourier and Wavelet analysis; source estimation at singletrial level; spatial resolution: point and fieldspread; spectral connectivity: coherence and phaselocking; possibly more… 