Software platform for clinical neuroimaging studies

This repository contains the files that generate Andy's Brain Book on ReadTheDocs.

ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.

Preprocessing pipeline on Brain MR Images through FSL and ANTs, including registration, skull-stripping, bias field correction, enhancement and segmentation.

Small Animal Magnetic Resonance Imaging via Python.

Introduction to dMRI

Utility MATLAB functions and wrappers for fMRI data analysis, mostly based in SPM12

PNH segmentation pipelines based on nipype

Code for performing static, dynamic and real-time shimming using external and internal MRI shim coils

FSL-R Interface package

The project is used to do preprocessing on brain MR images by using Nipype.

Tools for dealing with neuroimaging data in the BIDS structure

A Matlab-based software package for preprocessing the resting-state fMRI data

Probabilistic Threshold-Free Cluster Enhancement of Neuroimages

ElikoPy is Python library aiming at easing the processing of diffusion imaging for microstructural analysis.

A re-implementation of FSL's Brain Extraction Tool in Python

Cloud Based Interactive Visualization of Tractography Brain Connectome (CIVILITY) is an interactive visualization tool of brain connectome in the web.

General utility scripts, documentation, and analysis tutorials for Smith Lab.

Preprocessing Pipelines for EEG (MNE-python), fMRI (nipype), MEG (MNE-python/autoreject) data

atlasBREX: Automated averaged template-derived brain extraction in animal MRI