NITRC-CE
The NITRC Computational Environment is a freely downloadable, or pay-as-you-go, virtual computing cloud-based platform. It is pre-configured with popular neuroimaging tools such as AFNI, ANTS, FreeSurfer, FSL, C-PAC, and MRIcron to help you analyze your data quickly and easily. You can also add your commercial and open-source tools to use.
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Recently Registered Software

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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...

  • 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.

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