Brain Software Repository

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See also

• Bibliography of Institute of Biophysics, Chinese Academy of Sciences
• Bibliography of State Key Laboratory of Brain & Cognitive Sciences
• Bibliography of Sino-Danish Education Center
• Bibliography of ISP · Image and Signal Processing Group
• brainhack.org

NEURON

• Neuroimaging Informatics Tools and Resources Clearinghouse(NITRC)
• Cloud Computing for Neuroimaging
• Docker for Neuroimaging

The Ultimate Neuroscience Software Platform-Ecosystem-NeuroDebian

• NeuroDebian

  Provides a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others.

  
  [UNIX, GPL-3 license, noncommercial]

Data Management

• DataLad providing a data portal and a versioning system for everyone, DataLad lets you have your data and control it too.
  [Free for research use at nonprofit institutions]
• Brain Imaging Data Structure(BIDS)
  [Free for research use at nonprofit institutions]
• nibabel
  [Free for research use at nonprofit institutions]

Quality Control

• mriqc

Analysis

• AFNI Analysis of Functional NeuroImages.
  [Free for research use at nonprofit institutions]
• BrainVoyager Brain Innovation, Rainer Goebel.
  [Windows, Commercial]
• SPM By members & collaborators of the Wellcome Centre for Human Neuroimaging.
  [Matlab]
• Lyngby Lyngby is a Matlab program package for the analysis of functional neuroimages.
  [Matlab, Free for non-commercial use]
• bspmview bspmview is a graphical user interface for overlaying, thresholding, and visualizing 3D statistical neuroimages in MATLAB.
  [Matlab, UNIX/Windows, noncommercial]
• PORCUPINE Automatically create the code for your neuroimaging analysis pipeline.
  [Python, Unix/Windows, noncommercial]
• BIDS App BIDS App containing an instance of the Automatic Analysis neuroimaging.
  [Unix/Windows, noncommercial]
• Yale fMRI Analysis Package by Pawel Skudlarski from Yale NMR research group.
  [Matlab]
• fmriprep functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. Package from Poldrack lab at Stanford University for use at the Center for Reproducible Neuroscience (CRN), as well as for open-source software distribution.
  [Python, UNIX/Windows, noncommercial]
• Nipype An open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Package from Neuroimaging in Python team. More info link here.
  [Python, UNIX/Windows, noncommercial]
• Nitime Nitime is a library for time-series analysis of neuroscience data.
  [Python, UNIX/Windows, noncommercial]
• Popeye Popeye is a library for estimation of population receptive fields (pRF), accelerated with Cython and multiprocessing.
  [Python, UNIX/Windows, noncommercial]
• DSI Studio DSI Studio is an open-source diffusion MRI analysis tool that maps brain connections and correlates findings with neuropsychological disorders. It is a collective implementation of several methods, including DTI, QBI, DSI, generalized q-sampling imaging, q-space diffeomorphic reconstruction, diffusion MRI connectometry, and generalized deterministic fiber tracking.
  [Mac/Linux, Windows, Opensource]

Connectivity

• Brain Connectivity Toolbox The Brain Connectivity Toolbox (brain-connectivity-toolbox.net) is a MATLAB toolbox for complex-network analysis of structural and functional brain-connectivity data sets.
  [Matlab, noncommercial]

Visualization

• BrainVoyager Brain Innovation, Rainer Goebel.
  [Windows, Commercial]
• Caret Computerized Anatomical Reconstruction and Editing Toolkit. Program by Heather Drury and David Van Essen of Washington University School of Medicine.
  [UNIX-program, IRIX, noncommercial]
• GpetView Hiroshi Watabe's ANALYZE(tm) image viewer. From the homepage: "GpetView is light-weight image viewer based on Gtk+ library."
  [Unix (with Gtk+), free software (GNU)]
• mri3D (mri3dX) "mri3d is a general purpose program for 2 and 3-dimensional visualisation of structural MR images and functional localisations"
  The program is part of the BrainTools package.
  [Unix with Motif]
• MRIcro. Chris Rorden's Medical image viewer, conversion tool, and region of interest editor. [Windows 95/98/NT, freeware]
• Slice overlay. Matthew Brett's Image viewer.
  [Matlab, non-commercial]
• Niwidgets.
  [Python, non-commercial]
• Circos Visualization the network connectome online.

Machine Learning

• Scikit-Learn Scikit-Learn is a simple and efficient tools for machine learning in Python.
  [Python Windows/Linux, non-ommercial, BSD license]
• PYMC-Learn Pymc-learn provides probabilistic models for machine learning, in a familiar scikit-learn syntax.
  [Python Windows/Linux, non-ommercial, BSD license]
• Nilearn Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
  [Python Windows/Linux, non-ommercial]
• Pymvpa PyMVPA is a Python package intended to ease statistical learning analyses of large datasets.
  [Python Windows/Linux, non-ommercial]

Parallel Computing

• Dask Dask is a flexible library for parallel computing in Python.
  [Python Windows/Linux, non-ommercial]
  The manuscript of Ultimate guide to handle Big Datasets for Machine Learning using Dask (in Python)
• Joblib Joblib is a set of tools to provide lightweight pipelining in Python.
  [Python Windows/Linux, non-ommercial]
• Spark Apache Spark is a fast and general-purpose cluster computing system. It provides high-level APIs in Scala, Java, and Python that make parallel jobs easy to write, and an optimized engine that supports general computation graphs. It also supports a rich set of higher-level tools including Shark (Hive on Spark), MLlib for machine learning, graphX for graph processing, and Spark Streaming.
  [Python Windows/Linux, non-ommercial]
• Apache Hadoop The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.
  [Windows/Linux, non-ommercial]

Resources

• Tutorials for 2015 Berkeley practical neuroimaging
• The Pipeline of Processing fMRI data with Python Based on the Ecosystem NeuroDebian.
• Scientific Coding Resource
• brainlife.io
• COMPUTATIONAL NEUROSCIENCE
• NeuroHackAdemy
• Best websites for programmer
• Computer Sciences

	UCAS	University of Chinese Academy of Sciences
	SDC	Sino-Danish Education Center
	IBP	Institute of Biophysics, Chinese Academy of Sciences
	ISP	Image and Signal Processing group, University of Valencia

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Neuroscience && Neuroimaging Research Center