This chapter focuses on aspects of the philosophy of science, in particular the twentieth century views of Karl Popper and Thomas Kuhn. It briefly covers earlier aspects, including Francis Bacon and William Whewell who highlighted the need for, and influence of, subjective factors in science. In discussing Popper, it considers inductive and deductive reasoning and his falsification approach, while discussion of Kuhn focuses on his view of scientific paradigms, normal science, anomalies and crises, and paradigm shifts and scientific revolutions. It highlights both Popper’s and Kuhn’s views using neuroscience examples, including chemical synaptic transmission, animal electricity and adult neurogenesis. The conclusion is that there is no formal scientific method, no formula for discovery: scientists use, and need to use, a diversity of approaches.

This chapter considers induction, deduction and abduction as methods of obtaining scientific knowledge. The introductory section again ends by highlighting that there is no single method, and refers to claims that scientific reasoning uses various heuristics or rules of thumb based on the specific approach and the background information we have, and that we should recognise that this can introduce various errors of reasoning: by being aware of the potential for making these errors, we are better able to guard against making them. The bulk of the chapter then looks at specific logical fallacies, using neuroscience examples to illustrate them. These include ad hoc reasoning; begging the question; confusing correlation for causation; confirmation and disconfirmation biases; false dichotomies; false metaphors; the appeal to authority, tradition and emotion; the mereological fallacy; the naturalistic fallacy; and straw man arguments.

Computational neuroimaging is defined broadly as the use of neuroimaging to investigate the localization and representation of parameters in formal mathematical models. We focus upon models of behavior and neural processing that have been adopted widely in behavioral sciences and cognitive neuroscience, including reinforcement learning, predictive coding, decision theory (drift diffusion and evidence accumulation), population receptive field models, and encoding models (including artificial neural networks). The aim is not to explain all the technical details of the various models, but illustrate and discuss the added value of combining such models with neuroimaging.

Chapter 11 introduces basic EEG and MEG data analysis methods. It begins with an explanation of the noise components in EEG and MEG signals and discusses various methods of noise reduction, including filtering and independent component analysis (ICA). Spectral analysis, event-related response (ERR) analysis, and steady-state evoked response (ssER) analysis are then introduced. Each method is explained in plain language, followed by more detailed explanations to meet the different needs of beginners and advanced readers. Relevant statistical methods and data presentation formats are also introduced, using various data analysis platforms.

We present the main methods that are used to modulate brain activity directly. These methods are often used in combination or following up on neuroimaging experiments, in a means to test causal hypotheses. We include microstimulation, deep brain stimulation, focused ultrasound stimulation (FUS), transcranial magnetic stimulation (TMS) and its sub-types like single- and double-pulse and repetitive TMS. We end with transcranial current stimulation (TCS), also known as trancranial electric stimulation (TES), which comes in several variants such as transcranial direct current stimulation (TDCS) and transcranial alternating current stimulation (TACS).

Neurons generate electromagnetic fields as they communicate with each other. Chapter 9 introduces the electromagnetic field as a key concept overarching different electrophysiological brain activities. The concept corrects common misconceptions (e.g. "EEG is the sum of action potentials") and provides a common basis for data analysis of field signals. Basic properties of the field signal, amplitude, phase and frequency, are explained in plain language.

In addition, two major noninvasive techniques for measuring field activity, electroencephalography (EEG) and magnetoencephalography (MEG), are introduced. The advantages and disadvantages of the methods are discussed with a brief history of the techniques.

This method explains in an accessible way what the underlying principles are of magnetic resonance imaging, which underlies all structural imaging methods that are described in the next chapter.

This chapter sets the stage. We provide several examples of how neuroimaging findings have been covered in popular media, and the criticism that such coverage has elicited. This book intends to provide the knowledge and facts to understand the potential and proper use and mis-use of neuroimaging methods. We end with a brief overview of the different types of neuroimaging methods, and how they are organized with respect to spatial resolution, temporal resolution, and level of invasiveness.

We provide an introduction in the main pre-processing steps that are involved when analyzing imaging data: Correction for slice timing, motion correction, coregistration, normalization, and spatial smoothing

We discuss three more advanced statistical analysis approaches. First, the analysis of functional connectivity, including topics like directional and effective functional connectivity, modulations of connectivity by task (psychophysiological interactions), and resting-state fMRI. Second, we cover multivariate analyses and multi-voxel pattern analyses, and we discuss their potential and limitations to understand information processing in the brain. Third, we introduce the use of functional MRI adaptation as a means to measure neural selectivity.