PLINK - PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale genetic analyses.

MaCH - MaCH is a tool for haplotyping, genotype imputation and disease association analysis developed by Goncalo Abecasis and Yun Li.

NEURON - NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for conveniently building, managing, and using models in a way that is numerically sound and computationally efficient. It is particularly well-suited to problems that are closely linked to experimental data, especially those that involve cells with complex anatomical and biophysical properties. For a more detailed description see http://www.neuron.yale.edu/neuron/what_is_neuron

SPM - The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.

C-PAC - The Configurable Pipeline for the Analysis of Connectomes (C-PAC) is a configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion—without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.

3D Slicer - An extensible, cross-platform, totally open research platform for image computing.

BrainSuite - BrainSuite is a collection of open source software tools that enable largely automated processing of magnetic resonance images (MRI) of the human brain. The latest version of the BrainSuite software (v.21a) is available for download from the BrainSuite website (https://brainsuite.org/). This release includes a GUI for processing and visualization, tools to extract and parameterize cortex surface meshes, modules for automatic registration and labeling of brain volumes and surfaces, and distortion correction and coregistration of diffusion data with structural MRIs (available via the command line), for Windows, Mac OS X, and Linux platforms. BrainSuite source code is available under a GPLv2 license. BrainSuite is produced as a collaborative project between David Shattuck's research group at the UCLA Brain Mapping Center (http://shattuck.bmap.ucla.edu) and Richard Leahy's Biomedical Imaging Group at USC (http://neuroimage.usc.edu).

Solar Eclipse Imaging Genetics tools - We are developing software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. Official beta SOLAR Eclipse Version 8.3.X, adds multiple developments. This includes: Empirical pedigree from plink files, fast heritability (FPHI) and GWAS (NINGA) updates for CPU/GPU computing, more accurate p-value approximation for fast inference, polyclass_normalize function for multi-site homogenization and mega-analysis. Upcoming implements: CPU/GPU-based voxel-wise GWA using new HDF5 file format and cluster based statistical inference based on permutations. Source codes are distributed as a tarball or at github.com/kochunov/solar-eclipse The changes are described at http://solar-eclipse-genetics.org/

LONI Pipeline Environment - The LONI Pipeline is a free workflow application primarily aimed at neuroimaging researchers, but is useful for many other fields of science. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Visit http://pipeline.loni.usc.edu for more info. The Pipeline is distributed by the Laboratory of Neuro Imaging (http://www.loni.usc.edu/Software/Pipeline).

DWI/DTI Quality Control Tool: DTIPrep - DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing. Development of DTIPrep has been stopped, and DMRIPrep (within the DTI playground framework) is its successor (see https://github.com/NIRALUser/DTIPlayground)

scikit-learn - scikit-learn: machine learning in Python

Nipype: NIPY Pipeline and Interfaces - Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

NIPY Structural and Functional Analysis - Nipy aims to provide a complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

NiBabel - Read and write access to common neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, CIFTI-2, MINC1, MINC2, AFNI BRIK/HEAD, ECAT and Philips PAR/REC. In addition, NiBabel also supports FreeSurfer’s MGH, geometry, annotation and morphometry files, and provides some limited support for DICOM. NiBabel’s API gives full or selective access to header information (metadata), and image data is made available via NumPy arrays.

Connectome Viewer - Connectome Viewer is free, open source, cross-platform Python-based software application for visualization and analysis in connectome research. Features of the software include: * Connectome File Format including metadata, networks, surfaces, volumes, track files * Complex network analysis toolboxes * Modular plugin architecture for extensibility * Mayavi2 for 3D Scientific Visualization and Plotting * Interactive data manipulation and scripting capabilities * Neuroimaging and Diffusion in Python libraries

AFNI - AFNI is a set of C programs for processing, analyzing, and displaying FMRI data. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free for research purposes.

MRtrix - NOTE: this is the legacy version of MRtrix, and is no longer supported or maintained. To use the latest official version of MRtrix, please visit https://www.mrtrix.org MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines.

MRIcron - MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcron is a mature and useful tool, however you may want to consider the more recent MRIcroGL as an alternative.

Advanced Normalization Tools - Advanced Normalization Tools (ANTS) : Image registration with variable transformation models (elastic, diffeomorphic, unbiased) and similarity metrics (landmarks, cross-correlation, mutual information, optical flow). Designed for neuroscience and medical imaging researchers and users. Special capabilities include symmetric diffeomorphic normalization, optimal template creation and user-guided normalization.

DIPY Diffusion Imaging Analysis - DIPY is a free and open source software project for computational neuroanatomy. It focuses on diffusion magnetic resonance imaging (dMRI) analysis and tractography but also contains implementations of other computational imaging methods such as denoising and registration that are applicable to the greater medical imaging and image processing communities. Additionally, DIPY is an international project which brings together scientists across labs and countries to share their state-of-the-art code and expertise in the same codebase, accelerating scientific research in medical imaging. Twitter https://twitter.com/dipymri G+ http://bit.ly/dipymri

FreeSurfer - FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.

FSL - FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.