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FSL (the FMRIB Software Library) is a comprehensive library of analysis tools for functional, structural and diffusion MRI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford. For this NeuroImage special issue on “20 years of fMRI” we have been asked to write about the history, developments and current status of FSL. We also include some descriptions of parts of FSL that are not well covered in the existing literature. We hope that some of this content might be of interest to users of FSL, and also maybe to new research groups considering creating, releasing and supporting new software packages for brain image analysis.

The anatomy of language has been investigated with PET or fMRI for more than 20 years. Here I attempt to provide an overview of the brain areas associated with heard speech, speech production and reading. The conclusions of many hundreds of studies were considered, grouped according to the type of processing, and reported in the order that they were published. Many findings have been replicated time and time again leading to some consistent and undisputable conclusions. These are summarised in an anatomical model that indicates the location of the language areas and the most consistent functions that have been assigned to them. The implications for cognitive models of language processing are also considered. In particular, a distinction can be made between processes that are localized to specific structures (e.g. sensory and motor processing) and processes where specialisation arises in the distributed pattern of activation over many different areas that each participate in multiple functions. For example, phonological processing of heard speech is supported by the functional integration of auditory processing and articulation; and orthographic processing is supported by the functional integration of visual processing, articulation and semantics. Future studies will undoubtedly be able to improve the spatial precision with which functional regions can be dissociated but the greatest challenge will be to understand how different brain regions interact with one another in their attempts to comprehend and produce language.

FreeSurfer is a suite of tools for the analysis of neuroimaging data that provides an array of algorithms to quantify the functional, connectional and structural properties of the human brain. It has evolved from a package primarily aimed at generating surface representations of the cerebral cortex into one that automatically creates models of most macroscopically visible structures in the human brain given any reasonable T1-weighted input image. It is freely available, runs on a wide variety of hardware and software platforms, and is open source.

This review is aimed at celebrating the upcoming 20th anniversary of the birth of human functional near-infrared spectroscopy (fNIRS). After the discovery in 1992 that the functional activation of the human cerebral cortex (due to oxygenation and hemodynamic changes) can be explored by NIRS, human functional brain mapping research has gained a new dimension. fNIRS or optical topography, or near-infrared imaging or diffuse optical imaging is used mainly to detect simultaneous changes in optical properties of the human cortex from multiple measurement sites and displays the results in the form of a map or image over a specific area. In order to place current fNIRS research in its proper context, this paper presents a brief historical overview of the events that have shaped the present status of fNIRS. In particular, technological progresses of fNIRS are highlighted (i.e. from single-site to multi-site functional cortical measurements (images)), introduction of the commercial multi-channel systems, recent commercial wireless instrumentation and more advanced prototypes. ► The paper celebrates the 20th anniversary of functional fNIRS. ► Events that have shaped the present status of fNIRS are reported. ► fNIRS methodology has undergone consistent improvements over the years. ► The application of fNIRS in Medicine and basic research have been increasing. ► Technological development will augment fNIRS application in adults and infants.

Karl Friston began the SPM project around 1991. The rest is history

The core concept within the field of brain mapping is the use of a standardized, or “stereotaxic”, 3D coordinate frame for data analysis and reporting of findings from neuroimaging experiments. This simple construct allows brain researchers to combine data from many subjects such that group-averaged signals, be they structural or functional, can be detected above the background noise that would swamp subtle signals from any single subject. Where the signal is robust enough to be detected in individuals, it allows for the exploration of inter-individual variance in the location of that signal. From a larger perspective, it provides a powerful medium for comparison and/or combination of brain mapping findings from different imaging modalities and laboratories around the world. Finally, it provides a framework for the creation of large-scale neuroimaging databases or “atlases” that capture the population mean and variance in anatomical or physiological metrics as a function of age or disease. However, while the above benefits are not in question at first order, there are a number of conceptual and practical challenges that introduce second-order incompatibilities among experimental data. Stereotaxic mapping requires two basic components: (i) the specification of the 3D stereotaxic coordinate space, and (ii) a mapping function that transforms a 3D brain image from “native” space, i.e. the coordinate frame of the scanner at data acquisition, to that stereotaxic space. The first component is usually expressed by the choice of a representative 3D MR image that serves as target “template” or atlas. The native image is re-sampled from native to stereotaxic space under the mapping function that may have few or many degrees of freedom, depending upon the experimental design. The optimal choice of atlas template and mapping function depend upon considerations of age, gender, hemispheric asymmetry, anatomical correspondence, spatial normalization methodology and disease-specificity. Accounting, or not, for these various factors in defining stereotaxic space has created the specter of an ever-expanding set of atlases, customized for a particular experiment, that are mutually incompatible. These difficulties continue to plague the brain mapping field. This review article summarizes the evolution of stereotaxic space in term of the basic principles and associated conceptual challenges, the creation of population atlases and the future trends that can be expected in atlas evolution.

The goal of this review is to describe, from a personal perspective, the development and emergence of the resting state fMRI. In particular, various concepts derived from the resting state data are discussed in detail, including connectivity, amplitude of the fluctuations, analysis techniques, and use in clinical populations. We also briefly summarize our efforts in creating an open data sharing platform as well as both a journal and a conference dedicated to brain connectivity. All three projects are aimed at significantly increasing the impact of resting state fMRI developments and enabling large, collaborative science projects. ► The development and emergence of the resting state fMRI is presented. ► Various concepts derived from resting state fMRI are discussed. ► We summarize our efforts in creating an open data sharing platform. ► Formation of a journal and a conference dedicated to brain connectivity is discussed.

Functional connectivity between different brain regions can be estimated from MRI data by computing the temporal correlation of low frequency (<0.1Hz) fluctuations in the MRI signal. These correlated fluctuations occur even when the subject is “at rest” (not asked to perform any particular task) and result from spontaneous neuronal activity synchronized within multiple distinct networks of brain regions. This estimate of connectivity, however, can be influenced by physiological noise, such as cardiac and respiratory fluctuations. This brief review looks at the effect of physiological noise on estimates of resting-state functional connectivity, discusses ways to remove physiological noise, and provides a personal recollection of the early developments in these approaches. This review also discusses the importance of physiological noise correction and provides a summary of evidence demonstrating that functional connectivity does have a neuronal underpinning and cannot purely be the result of physiological noise.

In 2001, we published a paper on the representation of faces and objects in ventral temporal cortex that introduced a new method for fMRI analysis, which subsequently came to be called multivariate pattern analysis (MVPA). MVPA now refers to a diverse set of methods that analyze neural responses as patterns of activity that reflect the varying brain states that a cortical field or system can produce. This paper recounts the circumstances and events that led to the original study and later developments and innovations that have greatly expanded this approach to fMRI data analysis, leading to its widespread application.