This paper reviews the research conducted by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) on the development of new methodologies for the analysis of structural and functional magnetic resonance imaging (MRI) data. The majority of the research has been implemented as freely available software tools within FMRIB's Software Library (FSL). The paper is divided into several sections, each focusing on different aspects of MRI data analysis: 1. **Introduction**: Discusses the importance of MRI and functional MRI in investigating brain structure, function, development, and pathologies, and the need for flexible and scientifically informative analysis techniques. 2. **Functional MRI Analysis Research**: Focuses on the challenges and advancements in functional MRI analysis, including: - **FILM (FMRIB’s Improved Linear Model)**: A tool for voxelwise timeseries analysis that addresses temporal autocorrelation. - **FLAME (FMRIB’s Local Analysis of Mixed Effects)**: A tool for multi-level modeling and group analysis. - **FEAT (FMRIB’s Expert Analysis Tool)**: An advanced GUI-based tool for model-based FMRI analysis, including preprocessing, registration, and statistical analysis. - **Bayesian Inference on Constrained Linear Basis Sets**: Enhances HRF modeling for better activation detection. - **MELODIC (Multivariate Exploratory Linear Optimised Decomposition into Independent Components)**: A probabilistic ICA model for exploratory analysis. - **Spatial Mixture Modelling**: An alternative to null hypothesis testing for inference. 3. **Structural MRI Analysis Research**: Focuses on tools for quantitative measurements and processing in structural MRI data: - **BET (Brain Extraction Tool)**: For brain/non-brain segmentation. - **FAST (FMRIB’s Automated Segmentation Tool)**: For tissue-type segmentation and bias field correction. - **FLIRT (FMRIB’s Linear Image Registration Tool)**: For robust and accurate inter-modal image registration. - **MCFLIRT (Motion Correction)**: For rigid-body and non-rigid motion correction in FMRI data. - **SIENA (Structural Image Evaluation using Normalisation, of Atrophy)**: For quantitative measurement of brain change. 4. **Diffusion and White Matter Connectivity Analysis**: Introduces FDT (FMRIB’s Diffusion Toolbox) for statistical framework in diffusion tractography, allowing for the quantification of fiber connections. 5. **MR Physics-Related Research**: Discusses methods for correcting EPI distortion and simulating MRI experiments to validate and improve understanding of acquisition and analysis processes. The paper highlights the significant contributions of FMRIB in advancing the field of neuroimaging analysis and the practical implementation of these methodologies in FSL.This paper reviews the research conducted by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) on the development of new methodologies for the analysis of structural and functional magnetic resonance imaging (MRI) data. The majority of the research has been implemented as freely available software tools within FMRIB's Software Library (FSL). The paper is divided into several sections, each focusing on different aspects of MRI data analysis: 1. **Introduction**: Discusses the importance of MRI and functional MRI in investigating brain structure, function, development, and pathologies, and the need for flexible and scientifically informative analysis techniques. 2. **Functional MRI Analysis Research**: Focuses on the challenges and advancements in functional MRI analysis, including: - **FILM (FMRIB’s Improved Linear Model)**: A tool for voxelwise timeseries analysis that addresses temporal autocorrelation. - **FLAME (FMRIB’s Local Analysis of Mixed Effects)**: A tool for multi-level modeling and group analysis. - **FEAT (FMRIB’s Expert Analysis Tool)**: An advanced GUI-based tool for model-based FMRI analysis, including preprocessing, registration, and statistical analysis. - **Bayesian Inference on Constrained Linear Basis Sets**: Enhances HRF modeling for better activation detection. - **MELODIC (Multivariate Exploratory Linear Optimised Decomposition into Independent Components)**: A probabilistic ICA model for exploratory analysis. - **Spatial Mixture Modelling**: An alternative to null hypothesis testing for inference. 3. **Structural MRI Analysis Research**: Focuses on tools for quantitative measurements and processing in structural MRI data: - **BET (Brain Extraction Tool)**: For brain/non-brain segmentation. - **FAST (FMRIB’s Automated Segmentation Tool)**: For tissue-type segmentation and bias field correction. - **FLIRT (FMRIB’s Linear Image Registration Tool)**: For robust and accurate inter-modal image registration. - **MCFLIRT (Motion Correction)**: For rigid-body and non-rigid motion correction in FMRI data. - **SIENA (Structural Image Evaluation using Normalisation, of Atrophy)**: For quantitative measurement of brain change. 4. **Diffusion and White Matter Connectivity Analysis**: Introduces FDT (FMRIB’s Diffusion Toolbox) for statistical framework in diffusion tractography, allowing for the quantification of fiber connections. 5. **MR Physics-Related Research**: Discusses methods for correcting EPI distortion and simulating MRI experiments to validate and improve understanding of acquisition and analysis processes. The paper highlights the significant contributions of FMRIB in advancing the field of neuroimaging analysis and the practical implementation of these methodologies in FSL.