Functional magnetic resonance imaging (fMRI) has become the most popular method for imaging brain function. Handbook of Functional MRI Data Analysis provides a comprehensive and practical introduction to the methods used for fMRI data analysis. Using minimal jargon, this book explains the concepts behind processing fMRI data, focusing on the techniques that are most commonly used in the field. This book provides background about the methods employed by common data analysis packages including FSL, SPM and AFNI. Some of the newest cutting-edge techniques, including pattern classification analysis, connectivity modeling and resting state network analysis, are also discussed. Readers of this book, whether newcomers to the field or experienced researchers, will obtain a deep and effective knowledge of how to employ fMRI analysis to ask scientific questions and become more sophisticated users of fMRI analysis software.

This unique text presents a comprehensive review of methods for modeling signal and noise in magnetic resonance imaging (MRI), providing a systematic study, classifying and comparing the numerous and varied estimation and filtering techniques. Features: provides a complete framework for the modeling and analysis of noise in MRI, considering different modalities and acquisition techniques; describes noise and signal estimation for MRI from a statistical signal processing perspective; surveys the different methods to remove noise in MRI acquisitions from a practical point of view; reviews different techniques for estimating noise from MRI data in single- and multiple-coil systems for fully sampled acquisitions; examines the issue of noise estimation when accelerated acquisitions are considered, and parallel imaging methods are used to reconstruct the signal; includes appendices covering probability density functions, combinations of random variables used to derive estimators, and useful MRI datasets.

This book discusses the modeling and analysis of magnetic resonance imaging (MRI) data acquired from the human brain. The data processing pipelines described rely on R. The book is intended for readers from two communities: Statisticians who are interested in neuroimaging and looking for an introduction to the acquired data and typical scientific problems in the field; and neuroimaging students wanting to learn about the statistical modeling and analysis of MRI data. Offering a practical introduction to the field, the book focuses on those problems in data analysis for which implementations within R are available. It also includes fully worked examples and as such serves as a tutorial on MRI analysis with R, from which the readers can derive their own data processing scripts. The book starts with a short introduction to MRI and then examines the process of reading and writing common neuroimaging data formats to and from the R session. The main chapters cover three common MR imaging modalities and their data modeling and analysis problems: functional MRI, diffusion MRI, and Multi-Parameter Mapping. The book concludes with extended appendices providing details of the non-parametric statistics used and the resources for R and MRI data.The book also addresses the issues of reproducibility and topics like data organization and description, as well as open data and open science. It relies solely on a dynamic report generation with knitr and uses neuroimaging data publicly available in data repositories. The PDF was created executing the R code in the chunks and then running LaTeX, which means that almost all figures, numbers, and results were generated while producing the PDF from the sources.

This book discusses modelling and analysis of Magnetic Resonance Imaging (MRI) data of the human brain. For the data processing pipelines we rely on R, the software environment for statistical computing and graphics. The book is intended for readers from two communities: Statisticians, who are interested in neuroimaging and look for an introduction to the acquired data and typical scientific problems in the field and neuroimaging students, who want to learn about the statistical modeling and analysis of MRI data. Being a practical introduction, the book focuses on those problems in data analysis for which implementations within R are available. By providing full worked-out examples the book thus serves as a tutorial for MRI analysis with R, from which the reader can derive its own data processing scripts. The book starts with a short introduction into MRI. The next chapter considers the process of reading and writing common neuroimaging data formats to and from the R session. The main chapters then cover four common MR imaging modalities and their data modeling and analysis problems: functional MRI, diffusion MRI, Multi-Parameter Mapping and Inversion Recovery MRI. The book concludes with extended Appendices on details of the utilize non-parametric statistics and on resources for R and MRI data. The book also addresses the issues of reproducibility and topics like data organization and description, open data and open science. It completely relies on a dynamic report generation with knitr: The books R-code and intermediate results are available for reproducibility of the examples.

The popularity of magnetic resonance (MR) imaging in medicine is no mystery: it is non-invasive, it produces high quality structural and functional image data, and it is very versatile and flexible. Research into MR technology is advancing at a blistering pace, and modern engineers must keep up with the latest developments. This is only possible with a firm grounding in the basic principles of MR, and Advanced Image Processing in Magnetic Resonance Imaging solidly integrates this foundational knowledge with the latest advances in the field. Beginning with the basics of signal and image generation and reconstruction, the book covers in detail the signal processing techniques and algorithms, filtering techniques for MR images, quantitative analysis including image registration and integration of EEG and MEG techniques with MR, and MR spectroscopy techniques. The final section of the book explores functional MRI (fMRI) in detail, discussing fundamentals and advanced exploratory data analysis, Bayesian inference, and nonlinear analysis. Many of the results presented in the book are derived from the contributors' own work, imparting highly practical experience through experimental and numerical methods. Contributed by international experts at the forefront of the field, Advanced Image Processing in Magnetic Resonance Imaging is an indispensable guide for anyone interested in further advancing the technology and capabilities of MR imaging.

Spontaneous 'resting-state' fluctuations in neuronal activity offer insights into the inherent organisation of the human brain, and may provide markers for diagnosis and treatment of mental disorders. Resting state functional magnetic resonance imaging (fMRI) can be used to investigate intrinsic functional connectivity networks, which are identified based on similarities in the signal measured from different regions. From data acquisition to results interpretation, An Introduction to Resting State fMRI Functional Connectivity discusses a wide range of approaches without expecting previous knowledge of the reader, making it truly accessible to readers from a broad range of backgrounds. Supplemented with online examples to enable the reader to obtain hands-on experience working with data, the text also provides details to enhance learning for those already experienced in the field. The Oxford Neuroimaging Primers are written for new researchers or advanced undergraduates in neuroimaging to provide a thorough understanding of the ways in which neuroimaging data can be analysed and interpreted. Aimed at students without a background in mathematics or physics, this book is also important reading for those familiar with task fMRI but new to the field of resting state fMRI.