List of neuroimaging software

Neuroimaging software is used to study the structure and function of the brain. To see an NIH Blueprint for Neuroscience Research funded clearinghouse of many of these software applications, as well as hardware, etc. go to the NITRC web site.

• 3D Slicer Extensible, free open source multi-purpose software for visualization and analysis.
• aidScans, tumor volume estimation
• Amira 3D visualization and analysis software
• Analysis of Functional NeuroImages (AFNI)
• Analyze4D: A matlab GUI based tool designed for advanced ROI time course analysis and visualization(from Donders Institute)
• Analyze developed by the Biomedical Imaging Resource (BIR) at Mayo Clinic.
• Bioimage Suite.
• BrainMagix: Clinical neuroimaging software suite, with functional MRI, perfusion, diffusion and tractography modules, image fusion and segmentation tools.
• BESA (Brain Electrical Source Analysis)
• Bergen EEG-fMRI Toolbox plugin for EEGLab (remove fMRI gradients from simultaneous EEG-fMRI recordings)
• Brain Image Analysis Package
• BrainSuite,^[1] a collection of tools for extraction of cerebral cortex, segmentation and labeling brain volumes and surfaces, and distortion correction and coregistration of diffusion data with structural MRIs.
• BrainVISA
• BrainVoyager
• CamBA
• Camino Open-source toolkit for diffusion MRI.
• Caret Van Essen Lab, Washington University in St. Louis
• COINS (Collaborative Neuroimaging and Informatics Suite) developed by The Mind Research Network is a one stop neuroimaging/science/psychology research management toolsuite.
• CONN (functional connectivity toolbox)
• EEGLAB
• ExploreDTI ^[2] is a graphical toolbox, for exploratory diffusion (tensor) MRI and fiber tractography.
• Fiasco/FIAT (from CMU)
• Fieldtrip
• FMRIB Software Library (FSL)
• FMRLAB
• FreeSurfer
• GraphVar:^[3] A user-friendly toolbox for comprehensive graph analyses of functional brain connectivity
• IB Clinic by Imaging Biometrics
• ISAS (Ictal-Interictal SPECT Analysis by SPM)
• Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA)
• LONI Pipeline, Laboratory of Neuro Imaging, USC
• Mango,^[4] developed at the Research Imaging Center, University of Texas Health Science Center at San Antonio
• MINT LABS: Cloud-based data management and advanced Neuro-Imaging analysys system. www.mint-labs.com
• Medical Image Processing, Analysis, and Visualization software (MIPAV) , developed by BIRSS at the National Institutes of Health
• MNE : Magnetoencephalography (MEG) and Electroencephalography (EEG) in Python
• MNI MINC McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University
• MRIcro
• MRICloud,^[5] Center for Imaging Science, Whiting School of Engineering, The Johns Hopkins University
• MRIcron (Next generation of MRIcro)
• MRtrix, software for performing and analysing diffusion-weighted MRI white matter tractography in the presence of crossing fibres, using Constrained Spherical Deconvolution
• mrVista (from Stanford)
• MRVision
• MSmetrix, a CE- marked software as a service developed by icometrix. MSmetrix uses clinical MRI scans to measure lesion load and brain volume changes, mainly for MS patients. The service generates automated reports to be used in clinical practice.
• Net Station
• Neurophysiological Biomarker Toolbox
• Neuroreader™^[6] - a clinical software application that analyses MR brain scans, aimed at assisting the clinician in an assessment of structural MRI’s.
• NeuroLens
• NIAK, the NeuroImageing Analysis Kit
• NIfTI
• nilearn,^[7] Machine learning for Neuro-Imaging in Python
• NITRC The Neuroimaging Informatics Tools and Resources Clearinghouse. An NIH funded database of neuroimaging tools
• nordicICE
• Olea Medical: Olea Sphere 3.0, a CE - marked and FDA cleared product to automatize image processing for Neuroimaging and others fields and pathologies.
• Prism suite
• PyMVPA
• SHAring NeurOImaging Resources (Shanoir) is a neuroinformatics platform designed to share, archive, search and visualize neuroimaging data.
• Signed differential mapping (SDM)
• The Spinal Cord Toolbox (SCT) is the first comprehensive and open-source software for processing MR images of the spinal cord.^[8]
• Statistical parametric mapping (SPM)
• Stimulate (One of the earliest fMRI software package from CMRR at University of Minnesota)
• Tortoise^[9] Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble. A software package is for processing diffusion MRI data

References

1. Shattuck DW, Leahy RM (2002). "BrainSuite: An automated cortical surface identification tool". Medical Image Analysis. 6 (2): 129–142. doi:10.1016/S1361-8415(02)00054-3.
2. Leemans A, Jeurissen B, Sijbers J, and Jones DK. ExploreDTI: a graphical toolbox for processing, analyzing, and visualizing diffusion MR data. In: 17th Annual Meeting of Intl Soc Mag Reson Med, p. 3537, Hawaii, USA, 2009
3. Kruschwitz, J. D.; List, D.; Waller, L.; Rubinov, M.; Walter, H. (2015-04-30). "GraphVar: A user-friendly toolbox for comprehensive graph analyses of functional brain connectivity". Journal of Neuroscience Methods. 245: 107–115. doi:10.1016/j.jneumeth.2015.02.021.
4. Sadigh-Eteghad S, Majdi A, Farhoudi M, Talebi M, Mahmoudi J (2014). "Different patterns of brain activation in normal aging and Alzheimer's disease from cognitional sight: meta analysis using activation likelihood estimation". Journal of the Neurological Sciences. 343 (1): 159–66. doi:10.1016/j.jns.2014.05.066. PMID 24950901.
5. https://mricloud.org. Missing or empty |title= (help)
6. "Neuroreader™ – Clinical solution | Brainreader.net - neuroimaging software". brainreader.net. Retrieved 2016-01-27.
7. Abraham, A., Pedregosa, F., Eickenberg, M., Gervais, P., Mueller, A., Kossaifi, J., ... & Varoquaux, G. (2014). Machine learning for neuroimaging with scikit-learn. Frontiers in neuroinformatics, 8.
8. Cohen-Adad J, De Leener B, Benhamou M, Cadotte D, Fleet D, Cadotte A, Fehlings MG, Pelletier Paquette JP, Thong W, Taso M, Collins DL, Callot V, Fonov V. Spinal Cord Toolbox: an open-source framework for processing spinal cord MRI data. Proceedings of the 20th Annual Meeting of OHBM, Hamburg, Germany 2014:3633
9. C. Pierpaoli, L. Walker, M. O. Irfanoglu, A. Barnett, P. Basser, L-C. Chang, C. Koay, S. Pajevic, G. Rohde, J. Sarlls, and M. Wu, 2010, TORTOISE: an integrated software package for processing of diffusion MRI data, ISMRM 18th annual meeting, Stockholm, Sweden, #1597