Explore projects

Triplanar U-Net ensemble network (TrUE-Net) model for WMH segmentation

Pipeline for unbiased multimodal template construction from T1, T2 and DTI images.

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

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.

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

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.

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

A repo of folders containing Vagrant files that define useful Virtualbox recipes

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.

Implementation of Bayesian EstimatioN of CHange

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

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

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

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

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.

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.

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