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Top 57 neuroimaging open source projects

Brainiak

Brain Imaging Analysis Kit

✭ 232

python machine-learning distributed neuroscience neuroimaging

Freesurfer

Neuroimaging analysis and visualization suite

✭ 209

neuroimaging

Mriqc

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

✭ 152

python machine-learning neuroimaging

Awesome Deepneuroimage

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

✭ 145

deep-learning deep-neural-networks neuroimaging

Livianet

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"

✭ 143

python deep-learning deep-neural-networks convolutional-neural-networks neural-networks cnn medical-imaging image-segmentation theano convolutional-networks deep-learning-algorithms neuroimaging

Bids Specification

Brain Imaging Data Structure (BIDS) Specification

✭ 140

python standards neuroimaging

Intensity Normalization

normalize the intensity of several MR image contrasts with various routines

✭ 134

python neuroimaging

Mne Python

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

✭ 1,766

python Csound Document shell HTML javascript Makefile machine-learning visualization statistics neuroscience eeg neuroimaging meg electroencephalography magnetoencephalography electrocorticography ecog

Tedana

TE-dependent analysis of multi-echo fMRI

✭ 116

python neuroimaging

Neuropredict

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

✭ 87

python machine-learning scikit-learn easy-to-use report neuroimaging

Hitchhackers guide brain

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

✭ 85

eeg neuroimaging

Dltk

Deep Learning Toolkit for Medical Image Analysis

✭ 1,249

python deep-learning machine-learning tensorflow data-science neural-network deep-neural-networks neural-networks cnn ml medical-imaging medical neuroimaging

Nipype tutorial

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

✭ 76

python jupyter-notebook workflow neuroimaging

Ica Aroma

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

✭ 63

python data-driven neuroimaging

Extensionsindex

Slicer extensions index

✭ 36

python cross-platform image-processing qt segmentation medical-imaging registration neuroimaging

Slicerdmri

Diffusion MRI analysis and visualization in 3D Slicer open source medical imaging platform.

✭ 34

neuroimaging

Slicergitsvnarchive

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

✭ 896

python cross-platform image-processing qt segmentation medical-imaging 3d-printing registration neuroimaging

Nilearn

Machine learning for NeuroImaging in Python

✭ 712

python machine-learning decoding neuroimaging

Nipype

Workflows and interfaces for neuroimaging packages

✭ 557

python data-science big-data workflow-engine dataflow neuroimaging dataflow-programming

Fieldtrip

The MATLAB toolbox for MEG, EEG and iEEG analysis

✭ 481

matlab statistics analysis neuroscience eeg neuroimaging brain connectivity

Dipy

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.

✭ 417

python machine-learning segmentation tracking medical-imaging registration neuroimaging

Pycortex

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

✭ 383

javascript python neuroimaging

Fmriprep

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.

✭ 377

html image-processing neuroimaging

Dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC

✭ 364

research jpeg neuroscience dicom neuroimaging

Slicer

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

✭ 263

python image-processing qt segmentation medical-imaging 3d-printing registration neuroimaging

easylearn dev

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…

✭ 29

python HTML CSS matlab r Jupyter Notebook machine-learning deep-learning neuroimaging radiomics graphic-user-interface resting-state-fmri

dmipy

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

pTFCE

Probabilistic Threshold-Free Cluster Enhancement of Neuroimages

✭ 29

r shell Dockerfile statistical-inference neuroimaging fsl tfce cluster-enhancement

NeuroCore.jl

Core methods and structures for neuroscience research in Julia.

✭ 15

julia neuroscience neuroimaging neurophysiology

visualqc

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

✭ 56

python quality-control neuroscience medical-imaging registration alignment neuroimaging outlier-detection fmri mri-images cortex qc outlier-removal anatomical-mri freesurfer

NiMARE

Coordinate- and image-based meta-analysis in Python

✭ 107

python neuroimaging meta-analysis

fmriflows

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.

✭ 40

matlab Jupyter Notebook python shell Dockerfile Singularity HTML neuroimaging fmri bids

fslr

FSL-R Interface package

✭ 32

r neuroimaging fsl neuroimaging-analysis neuroimaging-data-science fslr

mrivis

medical image visualization library and development toolkit

✭ 19

python matlab Makefile visualization mismatch quality-control neuroscience similarity comparison mri registration alignment neuroimaging checkerboard

threeBrain

3D Visualization of Brain MRI

✭ 29

javascript r localization neuroimaging electroencephalography brain ecog ieeg template-brains mri-brain

Neuroimaging.jl

Neuroimaging in Julia

✭ 39

julia eeg neuroimaging electrophysiology

bids-matlab

MATLAB / Octave tools for BIDS datasets

✭ 37

matlab shell meg eeg mri octave pet neuroimaging bids ieeg

MIRACL

Multi-modal Image Registration And Connectivity anaLysis

✭ 23

python shell ImageJ Macro network neuroscience mri connectivity neuroimaging image-segmentation brain image-registration biomedical clarity atlases

bidscoin

BIDScoin converts your source-level neuroimaging data to BIDS

✭ 75

python mrs conversion dicom mri pet neuroimaging bids nifti data-sharing imaging data-standards brain-imaging nibabel deface multi-echo multi-echo-combine defacing parrec dcm2niix spec2nii

stagin

STAGIN: Spatio-Temporal Attention Graph Isomorphism Network

✭ 34

python attention neuroimaging fmri connectome explainability neurips gnn graph-neural-network stagin neurips2021

socialRL

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

✭ 19

matlab r Stan neuroimaging computational-modeling prediction-error decision-neuroscience

mne-bids

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

✭ 88

python TeX neuroscience meg eeg mne neuroimaging electroencephalography bids magnetoencephalography ieeg

Dcm2Bids

Reorganising NIfTI files from dcm2niix into the Brain Imaging Data Structure

✭ 109

python HTML Dockerfile neuroscience neuroimaging bids

clinica

Software platform for clinical neuroimaging studies

✭ 153

python matlab machine-learning scikit-learn neuroscience neuroimaging spm fsl ants freesurfer bids-format mrtrix3 brainweb

clinicadl

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

✭ 114

python deep-learning pytorch medical-imaging neuroimaging convolutional-neural-network brain-imaging alzheimer-disease

bidskit

Utility functions for working with DICOM and BIDS neuroimaging data

✭ 52

python Dockerfile conversion dicom mri neuroimaging fmri-preproc bids-format nifti-images

gifti

MATLAB/Octave GIfTI Library

✭ 16

c matlab Makefile neuroscience octave neuroimaging gifti

ColeAnticevicNetPartition

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

✭ 48

c matlab shell python Makefile neuroscience connectivity neuroimaging network-partitions brain brain-imaging

brainlit

Method container for computational neuroscience on brains.

✭ 20

python matlab Mathematica neuroscience neuroimaging

BrainMaGe

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

✭ 23

python Jupyter Notebook machine-learning deep-learning pytorch neuroimaging segmentation nih brain-extraction skull-stripping pytorch-lightning

nidb

NeuroInformatics Database

✭ 26

C++PHP c javascript CSS SWIG neuroscience neuroimaging neuroinformatics neuroinformatics-database

ENIGMA

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. 🤠

✭ 66