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Mne Python ⭐ 2,449

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

Slicer ⭐ 1,339

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

Deep Learning Toolkit for Medical Image Analysis

Nilearn ⭐ 1,076

Machine learning for NeuroImaging in Python

Awesome Neuroscience ⭐ 974

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

Slicergitsvnarchive ⭐ 883

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

Workflows and interfaces for neuroimaging packages

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.

Braindecode ⭐ 638

Deep learning software to decode EEG, ECG or MEG signals

Nibabel ⭐ 598

Python package to access a cacophony of neuro-imaging file formats

Pycortex ⭐ 534

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

Neuroimaging in Python FMRI analysis package

Brainiak ⭐ 315

Brain Imaging Analysis Kit

Intensity Normalization ⭐ 272

normalize the intensities of various MR image modalities

Bids Specification ⭐ 235

Brain Imaging Data Structure (BIDS) Specification

Pysurfer ⭐ 229

Cortical neuroimaging visualization in Python

Clinica ⭐ 201

Software platform for clinical neuroimaging studies

Neuromaps ⭐ 193

A toolbox for comparing brain maps

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.

Coordinate- and image-based meta-analysis in Python

TE-dependent analysis of multi-echo fMRI

Clinicadl ⭐ 146

Framework for the reproducible processing of neuroimaging data with deep learning methods

Nobrainer ⭐ 139

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

Livianet ⭐ 133

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"

Brainspace ⭐ 125

BrainSpace is an open-access toolbox that allows for the identification and analysis of gradients from neuroimaging and connectomics datasets | available in both Python and Matlab |

Smriprep ⭐ 111

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

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.

Bidscoin ⭐ 110

BIDScoin converts your source-level neuroimaging data to BIDS

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

The ENIGMA Toolbox is an open-source repository for accessing 100+ ENIGMA statistical maps, visualizing cortical and subcortical surface data, and relating neuroimaging findings to micro- and macroscale brain organization. 🤠

Neuropredict ⭐ 99

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

Nipype_tutorial ⭐ 97

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

Pcntoolkit ⭐ 91

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

Dyconnmap ⭐ 89

A dynamic connectome mapping module in python.

Ica Aroma ⭐ 84

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

Niworkflows ⭐ 81

Common workflows for MRI (anatomical, functional, diffusion, etc)

Dartbrains ⭐ 80

This repository is a Python package with all of the functions and python libraries required for the Dartmouth fMRI Analysis Course taught by Prof Luke Chang, PhD.

Neuroimaging in PyTorch

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

Nifti Image Converter ⭐ 64

🖼 A lightweight neuroimaging .nii to .png converter for Matlab and Python users

Dmriprep ⭐ 61

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

Bioexplorer ⭐ 61

The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration

Utility functions for working with DICOM and BIDS neuroimaging data

Whitematteranalysis ⭐ 56

White matter tractography clustering and more...

Halfpipe ⭐ 56

ENIGMA HALFpipe is a user-friendly software that facilitates reproducible analysis of fMRI data

Processing tools for high-resolution neuroimaging

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network

Extensionsindex ⭐ 52

Slicer extensions index

Connectomeviewer ⭐ 48

Software Application for the Visualization and Analysis of Multi-Modal Multi-Scale Network and Neuroimaging Data with Python

Netneurotools ⭐ 47

Useful tools from the Network Neuroscience Lab

Bidsonym ⭐ 47

a BIDS app for pseudo-anonymization of neuroimaging data

Neuromorph ⭐ 46

The NeuroMorph analysis and visualization toolkit

Fmriflows ⭐ 42

fmriflows is a consortium of many (dependent) fMRI analysis pipelines, including anatomical and functional pre-processing, univariate 1st and 2nd-level analysis, as well as multivariate pattern analysis.

Kaggle Trends 3rd Place Solution ⭐ 40

the 3rd place solution code of Kaggle TReNDS Neuroimaging (https://www.kaggle.com/c/trends-assessment-predic

Dynamical Neuroimaging Spatiotemporal Representations (DyNeuSR)

Small Animal Magnetic Resonance Imaging via Python.

A Python Toolbox for Multimode Neural Data Representation Analysis

Brain Coloring ⭐ 38

BrainPainter - Brain Visualisation Software

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

Brainstat ⭐ 37

A statistics and context decoding toolbox for neuroimaging.

Student version of NI-edu courses

Confounds ⭐ 35

Conquering confounds and covariates in machine learning

Nidm Specs ⭐ 34

Neuroimaging Data Model (NIDM): describing neuroimaging data and provenance

Learning From Brains ⭐ 34

Self-supervised learning techniques for neuroimaging data inspired by prominent learning frameworks in natural language processing + One of the broadest neuroimaging datasets used for pre-training to date.

Python package for power mapping and functional connectivity using DICS

Nipype Beginner S Guide ⭐ 33

Beginner's guide for Nipype

2018_materials ⭐ 32

Materials for Neurohackademy 2018 lectures, tutorials, etc.

Cortex_old ⭐ 32

Cortex - Deep learning tools for neuroimaging

Tools for analysis of brain imaging-derived networks, based on NetworkX

Multi-modal Image Registration And Connectivity anaLysis

Actflowtoolbox ⭐ 29

The Brain Activity Flow ("Actflow") Toolbox. Tools to quantify the relationship between connectivity and task activity through network simulations and machine learning prediction. Helps determine how connections contribute to specific brain functions.

A platform for analyzing neuroimaging data in Python

Hippmapp3r ⭐ 27

AICONSlab's hippocampal segmentation algorithm using CNNs

Sdcflows ⭐ 27

Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes

Neuroquery ⭐ 27

Implementation of the neuroquery encoding model that powers neuroquery.org

Tfce_mediation ⭐ 27

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

Voxelviz ⭐ 26

Visualization tool for fMRI data-sets using Plotly Dash

Reproman ⭐ 25

ReproMan (AKA NICEMAN, AKA ReproNim TRD3)

Framework for the reproducible classification of Alzheimer's disease using machine learning

Brainplotlib ⭐ 25

A lightweight package to plot brain surfaces with Python.

Pyradigm ⭐ 24

Research data management in biomedical and machine learning applications

Canonical ICA for fMRI

SC-GAN: 3D self-attention conditional GAN with spectral normalization for multi-modal neuroimaging synthesis

Brainlit ⭐ 23

Method container for computational neuroscience on brains.

Exercises for 2015 Berkeley practical neuroimaging class

medical image visualization library and development toolkit

Brainextractor ⭐ 20

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

Brainmage ⭐ 20

Brain extraction in presence of abnormalities, using single and multiple MRI modalities

Sdc Bids Smri ⭐ 20

Structural Neuroimaging Analysis in Python

Easylearn_dev ⭐ 20

Easylearn is designed for machine learning mainly in resting-state fMRI, radiomics and other fields (such as EEG). Easylearn is built on top of scikit-learn, pytorch and other packages. Easylearn can assist doctors and researchers who have limited coding experience to easily realize machine learning, e.g., (MR/CT/PET/EEG)imaging-marker- or other biomarker-based disease diagnosis and prediction, treatment response prediction, disease subtyping, dimensional decoding for transdiagnostic psychiatri

Sdc Bids Intromri ⭐ 19

Introduction to MRI and BIDS

Frontiers2013 ⭐ 19

Paper for special issue "Python in Neurosciences II"

Nibabies ⭐ 19

Processing tools for magnetic resonance images of infant brains

Trained Models ⭐ 19

Trained TensorFlow models for 3D image processing

Set of tools for downloading and accessing open-license neuroimaging data in a consistent format.

Assorted utilities for neuroimaging and cognitive science

Datalad Neuroimaging ⭐ 17

DataLad extension for neuroimaging research

Acerta Abide ⭐ 17

Deep learning using the ABIDE data

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