MNE : Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python

Deep Learning Toolkit for Medical Image Analysis

Multi-platform, free open source software for visualization and image computing.

Machine learning for NeuroImaging in Python

Workflows and interfaces for neuroimaging packages

The MATLAB toolbox for MEG, EEG and iEEG analysis

Pycortex is a python-based toolkit for surface visualization of fMRI data

DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

Brain Imaging Analysis Kit

Neuroimaging analysis and visualization suite

Multi-platform, free open source software for visualization and image computing.

A curated list of awesome deep learning applications in the field of neurological image analysis

This repository contains the code of LiviaNET, a 3D fully convolutional neural network that was employed in our work: "3D fully convolutional networks for subcortical segmentation in MRI: A large-scale study"

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain

Brain Imaging Data Structure (BIDS) Specification

TE-dependent analysis of multi-echo fMRI

LORIS is a web-accessible database solution for longitudinal multi-site studies.

normalize the intensity of several MR image contrasts with various routines

Easy and comprehensive assessment of predictive power, with support for neuroimaging features

Graph theory analysis of brain MRI data

A set of BIDS compatible datasets with empty raw data files that can be used for writing lightweight software tests.

Validator for the Brain Imaging Data Structure

A list of tutorials and other resources useful to learn open science and neuroimaging, EEG and MEG

Learn Nipype with these tutorial notebooks - go here to see them online -->

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

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

A framework for developing neural network models for 3D image processing.

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.