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.
• Amira 3D visualization and analysis software
• Analysis of Functional NeuroImages (AFNI)
• Analyze developed by the Biomedical Imaging Resource (BIR) at Mayo Clinic.
• 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.
• CamBA
• Caret Van Essen Lab, Washington University in St. Louis
• CONN (functional connectivity toolbox)
• EEGLAB
• ExploreDTI ^[2] is a graphical toolbox, for exploratory diffusion (tensor) MRI and fiber tractography.
• FMRIB Software Library (FSL)
• FreeSurfer
• ISAS (Ictal-Interictal SPECT Analysis by SPM)
• LONI Pipeline, Laboratory of Neuro Imaging, USC
• Mango,^[3] developed at the Research Imaging Center, University of Texas Health Science Center at San Antonio
• Neurophysiological Biomarker Toolbox
• nilearn,^[4] 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.
• 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.^[5]
• Statistical parametric mapping (SPM)
• Tortoise^[6] 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, US, 2009
3. ↑ 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. PMID 24950901. doi:10.1016/j.jns.2014.05.066. 
4. ↑ 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.
5. ↑ 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
6. ↑ 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