ITKArrayFire: ArrayFire-backed ITK pipelines
Spiderclaw: OpenBCI 3D-printable EEG headset files
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.
incdb-poc: INcDb Proof of Conept
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"
bids2pype: from bids data structure and model extension to info ready for nipype
3D-F-CNN-BrainStruct: This repository contains materials employed in our work to segment subcortical brain structures by employing a 3D fully Convolutional Neural Network.
life: Please use the new version of LiFE: www.github.com/brain-life/encode
C-PAC: Configurable Pipeline for the Analysis of Connectomes
SnPM-devel: Statistical NonParametric Mapping, development version
hcp2nipype-hack2015: The outcomes of the HCP to Nipype project at the OHBM Hackathon 2015.
CoSMoMVPA: A lightweight multivariate pattern analysis (MVPA) toolbox in Matlab / Octave
3D-brain-segmentation: This is a repository containing code to Paper "Optimized High Resolution 3D Dense-U-Net Network for Brain and Spine Segmentation" published at MDPI Applied sciences journal - https://www.mdpi.com/2076-3417/9/3/404 .
fastMRI: A large-scale dataset of both raw MRI measurements and clinical MRI images
neuropower-core: This repository contains the core functions from neuropower in a python package.
nilearn_tutorials: Nilearn tutorials for OHBM 2016 educational course
FSL-scripts: Script-framework using FSL, Freesurfer and AFNI functionality for automatization and high-throughput processing of MRI data in clustered environments.
eegtools: Collection of Python modules for EEG analysis. Includes EDF+ and BDF loaders, scalp plots and commonly used spatial filters.
quickNAT_pytorch: PyTorch Implementation of QuickNAT and Bayesian QuickNAT, a fast brain MRI segmentation framework with segmentation Quality control using structure-wise uncertainty
nsviewer: Neurosynth viewer
r-xnat: XNAT library for R
tvb-library: DEPRECATED: Use tvb-root. The science behind The Virtual Brain
microdraw: Collaborative vectorial annotation tool for ultra high resolution data
automaticanalysis: Automatic analysis
bidsify: Tool to convert raw MRI datasets to BIDS-compatible datasets
mindboggle: Automated anatomical brain label/shape analysis software (+ website)
raiders_data: An fMRI dataset from rich naturalistic audio/video stimulation (movie "Raiders of the lost Ark"). Origin: http://datasets.datalad.org/?dir=/labs/haxby/raiders
NeuroVault: Easy to use web database for statistical maps.
RegNet: Deformable Cross-modality MRI Registration Using 3D CNN
qa-athena: Quality assessment of Athena pipeline images
dcmstack: DICOM to Nifti conversion with meta data preservation
nidm-specs: Neuroimaging Data Model (NIDM): describing neuroimaging data and provenance
neuropower-web: sample size calculations for fMRI
quality-assessment-protocol: Scripts and documentation for the PCP's protocol for assessing data quality.
BROCCOLI: BROCCOLI: Software for Fast fMRI Analysis on Many-Core CPUs and GPUs
poldracklab-base: Repo for general-purpose code in the poldrack lab
relion: Image-processing software for cryo-electron microscopy
brain_segmentation: Implementation of VoxResNet for 3D brain segmentation
lddmmMASGD: This executable file is used for 3D brain MRI registration
nibabel: Python package to access a cacophony of neuro-imaging file formats
brainbrowser: Web-based visualization tools for neurological data.
fmri: :exclamation: This is a read-only mirror of the CRAN R package repository. fmri — Analysis of fMRI Experiments. Homepage: http://www.wias-berlin.de/software/imaging/
openBCI_BCI2k: a BCI2000 driver for the OpenBCI board
HCPpipelines: Processing pipelines for the HCP
cmp: Connectome Mapper
deepmedic: Efficient Multi-Scale 3D Convolutional Neural Network for Segmentation of 3D Medical Scans
pycortex: Pycortex is a python-based toolkit for surface visualization of fMRI data
datman: scripts for managing xnat, QC, and data analysis
pynetdicom: A pure Python DICOM network implementation
ANTs: Advanced Normalization Tools (ANTs)
_DEPRECATED_OpenBCI-V2hardware: This repository contains the core OpenBCI hardware and software frameworks.
neurokernel: Neurokernel Project
open-brain-consent: Making neuroimaging open from the grounds (consent form) and up (tools)
pyconto: Python Connectome Toolbox
OctaveMVPA: An All-in-One Princeton MVPA, AFNI-for-MATLAB, and SPM Distro: All Converted for Use in Octave
Suite2P: Tools for processing 2P recordings
SPM_connectome: Analysis of the data from the human connectome with SPM
freshMRI: a collection of resources to set up a neuroimaging data analysis environment
pybids: Python tools for querying and manipulating BIDS datasets.
csg_mri_pipelines: MRI preprocessing and analysis pipelines and tools for the study of disorders of consciousness
pyxnat: XNAT in Python
image-registration-cnn: [Incomplete] A PyTorch implementation of CNN based MRI image registration based on MICCAI 2018 paper "Linear and Deformable Image Registration with 3D Convolutional Neural Networks"
awesome-bci: Curated Collection of BCI resources
nidb: NeuroInformatics Database
repro-case-studies: Reproducibility case study contributions
Scalable-Brain-Atlas: Source code of the Scalable Brain Atlas website (scalablebrainatlas.incf.org)
fslr: FSL-R Interface package
pyhrf: PyHRF is a set of tools to analyze fMRI data and specifically study hemodynamics.
nipype: Workflows and interfaces for neuroimaging packages
bctpy: brain connectivity toolbox for python
BEaST: C implementation of Brain Extraction based on nonlocal Segmentation Technique
visbrain: A multi-purpose GPU-accelerated open-source suite for brain data visualization
brainx: Tools for analysis of brain imaging-derived networks, based on NetworkX
brain-age-prediction: Notes on developmental trajectories, predicting brain maturation, effects of head motion on sMRI, and qMRI and brain development
clij: CLIJ is deprecated. Visit CLIJ2
heudiconv: A flexible DICOM converter for organizing brain imaging data into structured directory layouts
myconnectome: Code for the myconnectome project
ICA-AROMA: ICA-AROMA Software Package: a data-driven method to identify and remove head motion-related artefacts from functional MRI data.
PowerGrid: GPU accelerated non-Cartesian magnetic resonance imaging reconstruction toolkit
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.
3DUnetCNN: Pytorch 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation
projectMatlab: Interface R, Matlab, SPM
afni: Official AFNI source and documentation
workbench: Connectome Workbench
dcm2niix: dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
Z-Brain: Z-Brain Viewer and Analysis Scripts for MAP-Mapping
fieldtrip: The MATLAB toolbox for MEG, EEG and iEEG analysis
niak: GNU Octave library for connectivity analysis in large fMRI datasets
fmri-analysis-vm: A VM setup for use in fMRI analysis and education
fs-cwl: Common workflow language wrappers and workflow for FreeSurfer
CiftiLib: C++ Library for reading and writing CIFTI-2 and CIFTI-1 files
QUIT: A set of tools for processing Quantitative MR Images
spm12w: Spm12w is a set of tools and scripts to automate various aspects of fMRI preprocessing and GLM analysis in SPM12.
biananes: Scalable fMRI Data Analysis
epitome: scriptit modules for fmri analysis
grabbit: get grabby with file trees
pipeline-scheduler: Flask server to schedule and process XNAT pipelines with OpenStack
zindex: libznz with zindex
ACE: Tools for automatic extraction of activation coordinates from published neuroimaging articles.
nipy: Neuroimaging in Python FMRI analysis package
studycentric: StudyCentric - research DICOM viewer
nidata: Set of tools for downloading and accessing open-license neuroimaging data in a consistent format.
pipedream: PipeDream - open source neuroimaging pipelines
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