Explore projects

FileTrees provide a way to define the content of a structured directory. This can be very handy when defining input/output files for a pipeline.

Code for the generation, processing, and analysis of imaging confounds in UKB Biobank.

FSL Tools for MR Spectroscopy - Fitting/Plotting/Simulations/etc.

Code for inferring PRObabilistic FUnctional MOdes. See DOI: 10.1016/j.neuroimage.2015.01.013 and DOI: 10.1016/j.neuroimage.2020.117226.

FSL documentation

Tensor Image Registration Library - a modular general-purpose image registration framework for Python with prebaked scripts for histology-to-MRI registration.

Utility to download and install FSL modules - patch files, atlases, standard templates, example data, etc etc.

Talks and Jupyter notebook-based practicals for the 2018 WIN PyTreat

UK Biobank imaging pipeline adaptations for use in a real-world memory clinic sample at the Oxford Brain Health Clinic

Remove stupidly high intensities from MRI images which might negatively affect registration.

Python-based asymmetric fibre orientation distributions (aFODs) estimation library

FSL MELODIC results viewer. Specifically intended for use with training the FIX tool.

Code for "Harmonising large-scale imaging databases to provide integrated assessments of the role of white matter hyperintensities in cognitive aging." Discovery Award Project

BRC-EM Transparent and Reproducible fMRI Analysis guide. Code and tutorials for analysis of a typical functional magnetic resonance imaging (fMRI) task data set collected as part of a study adopted by the University of Oxford Health Biomedical Research Centre (BRC) Experimental Medicine theme (BRC-EM).

Version 1.5 of the Pipeline for brain imaging processing of UK Biobank.

Pipeline developed by Fidel Alfaro Almagro, Steve Smith and Mark Jenkinson.

Contributions by FMRIB Analysis Group, University of Oxford.

Multimodal Image Segmentation Tool