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Mne Python ⭐ 2,449

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

Awesome Neuroscience ⭐ 974

A curated list of awesome neuroscience libraries, software and any content related to the domain.

Fieldtrip ⭐ 782

The MATLAB toolbox for MEG, EEG and iEEG analysis

Dcm2niix ⭐ 746

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

Braindecode ⭐ 638

Deep learning software to decode EEG, ECG or MEG signals

Brainiak ⭐ 315

Brain Imaging Analysis Kit

Clinica ⭐ 201

Software platform for clinical neuroimaging studies

Neuromorphic Computing Guide ⭐ 191

Learn about the Neumorphic engineering process of creating large-scale integration (VLSI) systems containing electronic analog circuits to mimic neuro-biological architectures.

Dcm2bids ⭐ 146

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

Canlabcore ⭐ 135

Core tools required for running Canlab Matlab toolboxes. The heart of this toolbox is object-oriented tools that enable interactive analysis of neuroimaging data and simple scripts using high-level commands tailored to neuroimaging analysis.

Mne Bids ⭐ 110

MNE-BIDS is a Python package that allows you to read and write BIDS-compatible datasets with the help of MNE-Python.

Expyriment ⭐ 109

Platform-independent lightweight Python library for designing and conducting timing-critical behavioural and neuroimaging experiments

A Python implementation of the Preprocessing Pipeline (PREP) for EEG data

Braingraph ⭐ 94

Graph theory analysis of brain MRI data

Pcntoolkit ⭐ 91

Toolbox for normative modelling and spatial inference of neuroimaging data. https://pcntoolkit.readthedocs.io/en/latest/

Openneuro ⭐ 91

A free and open platform for analyzing and sharing neuroimaging data

Dyconnmap ⭐ 89

A dynamic connectome mapping module in python.

MATLAB application for fNIRS data processing and visualization

Visualqc ⭐ 68

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

The open source toolbox for reproducible diffusion MRI-based microstructure estimation

Micaopen ⭐ 58

Open Scripts and pipelines from the Multimodal Imaging and Connectome Analysis Lab at the Montreal Neurological Institute

Code to analyse structural covariance brain networks using python.

SPM (Statistical Parametric Mapping) - Development Version

Netneurotools ⭐ 47

Useful tools from the Network Neuroscience Lab

Network_tda_tutorial ⭐ 43

This repository is dedicated for the tutorial on network and topological neuroscience.

A framework for real-time brain signal streaming with MNE-Python.

Coleanticevicnetpartition ⭐ 37

Public release of The Cole-Anticevic Brain-wide Network Partition (CAB-NP)

Confounds ⭐ 35

Conquering confounds and covariates in machine learning

Python package for power mapping and functional connectivity using DICS

APPIAN is an open-source automated software pipeline for analyzing PET images in conjunction with MRI. The goal of APPIAN is to make PET tracer kinetic data analysis easy for users with moderate computing skills and to facilitate reproducible research.

Assemblynet ⭐ 31

AssemblyNet: 3D Whole Brain MRI segmentation pipeline

Vscode Neuro Viewer ⭐ 30

Check metadata and visualize neuroimages within VSCode.

Multi-modal Image Registration And Connectivity anaLysis

Please use the new version of LiFE: www.github.com/brain-life/encode

Subject-wise networks from structural MRI, both vertex- and voxel-wise features (thickness, GM density, curvature, gyrification)

Hippmapp3r ⭐ 27

AICONSlab's hippocampal segmentation algorithm using CNNs

Tfce_mediation ⭐ 27

Fast regression and mediation analysis of vertex or voxel MRI data with TFCE

NeuroInformatics Database

Online_neuroimaging_resources ⭐ 24

a laundry list of resources for MRI, fMRI, EEG, MEG...

Pyradigm ⭐ 24

Research data management in biomedical and machine learning applications

BRAPH 2.0 is a comprehensive software package for the analysis and visualization of brain connectivity data, offering flexible customization, rich visualization capabilities, and a platform for collaboration in neuroscience research.

Brainlit ⭐ 23

Method container for computational neuroscience on brains.

MATLAB/Octave GIfTI Library

An easy to use decoding toolbox for Matlab users.

medical image visualization library and development toolkit

Brainextractor ⭐ 20

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

Workstation ⭐ 19

Janelia Workstation

Frontiers2013 ⭐ 19

Paper for special issue "Python in Neurosciences II"

Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets.

Openscienceroom2019 ⭐ 16

Schedule and resources from the OHBM Open Science Room: Rome 2019

Spm Docs ⭐ 15

SPM Documentation

Airflow Imaging Plugins ⭐ 14

Set of plugins helping to work with imaging data in Airflow.

An Introduction to Programming for Psychologists & Neuroscientists Course at Dartmouth PBS

Imaging Transcriptomics ⭐ 13

A package, and script, to perform imaging transcriptomics on a neuroimaging scan.

Sourcemesh ⭐ 13

A multipurpose matlab-based MEG/EEG overlay & network plotter

Icvmapp3r ⭐ 12

AICONSlab's brain extraction (skull-stripping) algorithm using CNNs

Socialrl ⭐ 12

Code and data for Zhang, Lengersdorff et al. (2020)

Brainspell Neo ⭐ 12

Working on a new version of Brainspell (an open-source platform for neuroimaging literature) to make a public JSON API that collaborators can contribute to, switch out the stack for better scalability, and provide statistical features to better conduct meta-analyses.

Getyourbraintogether ⭐ 12

Get Your Brain Together Neuroimage Registration Workshops and Hackathons

NeuroImaging Quality Control (niQC)

Neuroformats.jl ⭐ 11

Handling of structural neuroimaging file formats for Julia.

Neural_pre_processing ⭐ 11

Neural Pre Processing is an end-to-end weakly supervised learning approach for converting raw head MRI images to intensity-normalized, skull-stripped brain in a standard coordinate space

Conn_tools ⭐ 11

Some tools for the extraction and plot of second-level ROI-to-ROI results from CONN Toolbox

Neuroscience Data Structure ⭐ 10

Space for discussion of a standardized structure (directory layout + metadata) for experimental data in systems neuroscience, similar to the idea of BIDS in neuroimaging

Meg Group Decode ⭐ 10

Train Wavenet-based group-level models on MEG data, and uncover neuroscientifically interpretable information.

Histogram-weighted Networks for Connectivity & Advanced Analysis in Neuroscience

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance

The Brain Predictability toolbox (BPt), is a python based Machine Learning library designed primarily for tabular and neuroimaging specific neuroimaging data but can easily be generalized further.

React Fmri ⭐ 8

REACT: Receptor-Enriched Analysis of functional Connectivity by Targets

Module to read Biosemi BDF files with the Julia programming language

Brainwave.jl ⭐ 8

Julia functions to process electroencephalographic (EEG) recordings

Ironsmithqsm ⭐ 8

Ironsmith is a comprehensive, fully automated pipeline for creating and processing Quantitative Susceptibility Maps (QSM), extracting QSM based iron concentrations from subcortical and cortical brain regions and evaluating the quality of QSM data using SNR measures and assessment of outlier regions on phase images.

Brainlife.io Documentation

Package for analysing functional near-infrared spectroscopy (fNIRS) data

Spm Hospital Preproc ⭐ 7

A MATLAB toolbox for various preprocessing operations (registration, reslicing, denoising, segmentation, etc.) of neuroimaging data. Builds on the SPM12 software.

Bids Nirs Tapping ⭐ 7

Example fNIRS BIDS dataset

Neuroformats Rs ⭐ 6

Handling of structural neuroimaging file formats for Rust.

Brain Coloring Website ⭐ 6

BrainPainter Website code

Versatile Electrode localization fRAmework

Bayesfactorfmri ⭐ 6

BayesFactorFMRI is a tool developed with R and Python to allow neuroimaging researchers to conduct Bayesian second-level analysis of fMRI data and Bayesian meta-analysis of fMRI images with multiprocessing.

group sequential tests for neuroimaging

Mni_to_atlas ⭐ 5

A simple Python-based tool for finding brain atlas regions based on MNI coordinates.

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