PNiP

Perceptual Neuroimaging in Practice

Format

During term time we meet Fridays 10am for sessions lasting 1-2hrs.

Generally, each topic is covered by two sessions, the first being an (interactive) lecture introducing the topic and leading up to a coding homework. The second session is a flipped classroom in which we review the coding homework and any problems you ran into. The previous instance was all online, but we hope to meet in person (or hybrid) for the next one.


Term 1

PNiP is split into two terms. Roughly, the first term emulates SPM's Methods for Dummies and covers the basics. Topics range from programming a minimal experiment, the HRF, preprocessing, quality assurance and GLMs to optimising designs and statistical considerations. Most topics during the first term will be presented by participants.

Your presentation should last 30-45 minutes (plus 15 minutes discussion). It should cover an intuitive explanation of the theory as well as a walk-through of the practical implementation in SPM12, which should culminate in a coding homework. Fear not - you can always ask an expert for help and don't have to start from scratch. You can build on slides of your predecessors or MfD. However, you should make a real effort to learn about 'your' topic, so everyone will profit from each other.


Term 2

The second term covers more advanced topics, like tractography, surface reconstruction, MVPA, RSA, deep nets and encoding models. These will mostly be presented by local and international experts on the respective topic. Typically, coding exercises will require installing additional software which will be provided during the first session covering a topic.


In general

-> We will provide example data for the practical parts. However, if you have data of your own, feel free to apply what you learned to that!

-> At least one expert will be present for each session (PI with MRI experience, usually Ben)

-> There is time for questions. These can be related to the topic, or unrelated 'methods clinics'. There is also time for presentations of your own work. Just let Ben know if you would like to use a meeting for that.

Course requirements

Must have

Laptop or computer

Working installations of MATLAB and SPM12 (let Ben know if this is an issue)

Willingness to participate actively and regularly


Recommended

Helpful background reading (let Ben know if you have issues accessing these):

Handbook of Functional MRI Data Analysis by Poldrack et al. is an excellent conceptual introduction

Statistical Analysis of fMRI Data by Ashby covers many topics in depth and code

All participants are encouraged to work through these coding exercises, to get into neuroimaging data in MATLAB. If you are new to programming and/or MATLAB, I further recommend working through Chapter 2 in Pascal Wallisch's MATLAB for Neuroscientists.