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 (from Harvard, multi-purposes processing software including diffusion tensor imaging tractography)
• aidScans, tumor volume estimation [1]

• Analysis of Functional NeuroImages (AFNI) [2]
• Analyze4D: A matlab GUI based tool designed for advanced ROI time course analysis and visualization(from Donders Institute) [3]
• Analyze developed by the Biomedical Imaging Resource (BIR) at Mayo Clinic. AnalyzeDirect homepage
• Bioimage Suite.
• BrainMagix
• BESA (Brain Electrical Source Analysis) [4]
• Bergen EEG-fMRI Toolbox plugin for EEGLab (remove fMRI gradients from simultaneous EEG-fMRI recordings)
• Brain Image Analysis Package [5]
• BrainVISA [6]
• BrainVoyager [7]
• CamBA [8]
• Camino Open-source toolkit for diffusion MRI. Camino homepage
• Caret [9] 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.
• Fiasco/FIAT (from CMU)
• FMRIB Software Library (FSL) [10]
• FMRLAB
• FreeSurfer [11]
• ISAS (Ictal-Interictal SPECT Analysis by SPM)
• Leipzig Image Processing and Statistical Inference Algorithms (LIPSIA) [12]
• LONI Pipeline Laboratory of Neuro Imaging, UCLA
• Mango, developed at the Research Imaging Center, University of Texas Health Science Center at San Antonio
• Medical Image Processing, Analysis, and Visualization software (MIPAV) [13], developed by BIRSS[14] at the National Institutes of Health
• MNI MINC McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University
• MRIcro
• MRIcron (Next generation of MRIcro)

• mrVista (from Stanford)
• MRVision
• Net Station [15]
• Neuroimaging software installation support
• NeuroLens
• NIfTI [16]
• NITRC The Neuroimaging Informatics Tools and Resources Clearinghouse. An NIH funded database of neuroimaging tools [17]
• nordicICE
• Olea Medical: PerfScape & NeuroScape (see also the Olea Medical website)
• Prism suite
• PyMVPA [18]
• SHAring NeurOImaging Resources (Shanoir) is a neuroinformatics platform designed to share, archive, search and visualize neuroimaging data. Shanoir homepage
• Signed differential mapping (SDM) [19]
• Statistical parametric mapping (SPM) [20]
• Stimulate (One of the earliest fMRI software package from CMRR at University of Minnesota)