http://software.incf.net/search/ Latest changes to your search for: Showing all registered software en-us Wed, 24 Mar 2010 10:13:45 -0000 http://software.incf.org/software/eeglab Open Source Matlab Toolbox for Electrophysiological Research.. http://software.incf.org/software/eeglab http://software.incf.org/software/myfirstneuron .. http://software.incf.org/software/myfirstneuron http://software.incf.org/software/dchip Windows software package for probe-level (e.g.. http://software.incf.org/software/dchip http://software.incf.org/software/neuroconstruct neuroConstruct has been designed to simplify creation, visualisation, simulation and analysis of complex networks of biologically realistic neurons. http://software.incf.org/software/neuroconstruct http://software.incf.org/software/imagej ImageJ is a Java-based image processing and analysis program developed at the National Institutes of Health. http://software.incf.org/software/imagej http://software.incf.org/software/xml-based-clinical-experiment-data-exchange-schema The XCEDE schema provides an extensive metadata hierarchy for describing and documenting research and clinical studies. http://software.incf.org/software/xml-based-clinical-experiment-data-exchange-schema http://software.incf.org/software/finding-information-in-neural-data-find An open-source analysis toolbox for multiple-neuron recordings and network simulations.. http://software.incf.org/software/finding-information-in-neural-data-find http://software.incf.org/software/brainsuite2 BrainSuite2 is used for cortical surface extraction.. http://software.incf.org/software/brainsuite2 http://software.incf.org/software/allen-brain-atlas-api 2D and 3D Programmatic Access to the ABA Mouse Brain Project.. http://software.incf.org/software/allen-brain-atlas-api http://software.incf.org/software/lddmm-volume LDDMM-volume provides direct comparison and quantization of morphometric changes in shapes. http://software.incf.org/software/lddmm-volume http://software.incf.org/software/fastica The standard software for independent component analysis (ICA). http://software.incf.org/software/fastica http://software.incf.org/software/xnbc-v910 XNBC is an open source simulation tool for the neuroscientists interested in simulating biological neural networks using a user friendly tool. http://software.incf.org/software/xnbc-v910 http://software.incf.org/software/matching-pursuit-in-stochastic-dictionaries adaptive time-frequency decomposition in stochastic Gabor dictionaries by means of a computationally optimized matching pursuit algorithm.. http://software.incf.org/software/matching-pursuit-in-stochastic-dictionaries http://software.incf.org/software/neuromatic NeuroMatic is a collection of Igor Pro functions for analyzing and acquiring electrophysiological data. http://software.incf.org/software/neuromatic http://software.incf.org/software/bsmart A Matlab/C toolbox for Analyzing Brain Circuits.. http://software.incf.org/software/bsmart http://software.incf.org/software/bioconductor Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. http://software.incf.org/software/bioconductor http://software.incf.org/software/genesis The GENESIS simulator (the GEneral NEural SImulation System) is used for creating biologically realistic computer models of neural systems.. http://software.incf.org/software/genesis http://software.incf.org/software/pgenesis PGENESIS is a software package that enables the GENESIS neural simulator to run on a variety of parallel machines (including multi-core workstations). http://software.incf.org/software/pgenesis http://software.incf.org/software/brian-2 Brian is a simulator for spiking neural networks, written in Python.. http://software.incf.org/software/brian-2 http://software.incf.org/software/wfu_pickatlas WFU_PickAtlas provides a method for generating ROI masks based on the Talairach Daemon database. http://software.incf.org/software/wfu_pickatlas http://software.incf.org/software/minc-medical-image-netcdf MINC is primarily a file format and a 3 level API for medical image analysis with a particular focus on the needs of research. http://software.incf.org/software/minc-medical-image-netcdf http://software.incf.org/software/music C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime. http://software.incf.org/software/music http://software.incf.org/software/pynn-3-2 A Python package for simulator-independent specification of neuronal network models. http://software.incf.org/software/pynn-3-2 http://software.incf.org/software/itools-resourceome iTools is a meta-resource for managing, traversal, discovery and exploration of data, tools and services via human and machine interfaces. http://software.incf.org/software/itools-resourceome http://software.incf.org/software/loni-viz LONI_Viz, is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views.. http://software.incf.org/software/loni-viz http://software.incf.org/software/shiva Synchronized Histological Image Viewing Architecture.. http://software.incf.org/software/shiva http://software.incf.org/software/neurospaces Development center for software components of a neuroscience simulator. http://software.incf.org/software/neurospaces http://software.incf.org/software/neurofitter Neurofitter is software for parameter tuning of electrophysiological neuron models. http://software.incf.org/software/neurofitter http://software.incf.org/software/mean-machine Matlab-based software for analyzing EEG data.. http://software.incf.org/software/mean-machine http://software.incf.org/software/sa3d-spatial-analysis-3d Matlab GUI for the modelling and analysis of neuronal positioning in three dimensions.. http://software.incf.org/software/sa3d-spatial-analysis-3d http://software.incf.org/software/topographica Topographica is a software package for computational modeling of neural maps, such as those in sensory and motor systems in mammals. http://software.incf.org/software/topographica http://software.incf.org/software/csdplotter A MATLAB toolbox for computing the Current Source Density (CSD), currently for one dimensional electrode arrays. http://software.incf.org/software/csdplotter http://software.incf.org/software/pyentropy A Python library for estimation of entropy and information theoretic quantities. http://software.incf.org/software/pyentropy http://software.incf.org/software/wfu_bpm The WFU Biological Parametric Mapping (WFU_BPM) toolbox performs SPM analysis with voxel-wise imaging covariates.. http://software.incf.org/software/wfu_bpm http://software.incf.org/software/ibraintm iBrain™ is an easy-to-use processing and visualisation platform designed to explore functional fMRI and other neuroimaging data.. http://software.incf.org/software/ibraintm http://software.incf.org/software/mne-minimum-norm-current-estimates The MNE software has been developed to compute cortically-constrained L2 minimum-norm current estimates and associated dynamic statistical parametric maps from MEG and EEG data, optionally constrained by fMRI. http://software.incf.org/software/mne-minimum-norm-current-estimates http://software.incf.org/software/brahms Framework for modular model development. http://software.incf.org/software/brahms http://software.incf.org/software/openelectropy The OpenElectrophy project aims to simplify data and analysis sharing for intra- and extra-cellular recordings.. http://software.incf.org/software/openelectropy http://software.incf.org/software/information-breakdown-toolbox An open source software package for the information theoretic analysis of neural data.. http://software.incf.org/software/information-breakdown-toolbox http://software.incf.org/software/pcsim PCSIM is a tool for distributed simulation of heterogeneous networks composed of different point neuron models. http://software.incf.org/software/pcsim http://software.incf.org/software/pydstool Simulation and analysis scripting environment environment for dynamical systems models of biophysical systems (ODEs, DAEs, maps, and hybrid systems).. http://software.incf.org/software/pydstool http://software.incf.org/software/whole-brain-catalog An open source multi-scale virtual catalog of the mouse brain.. http://software.incf.org/software/whole-brain-catalog http://software.incf.org/software/mbat Mouse BIRN Atlasing Toolkit.. http://software.incf.org/software/mbat http://software.incf.org/software/carmen CARMEN is a virtual laboratory for neurophysiology - enabling collaborative exploitation of data, analysis code and expertise. http://software.incf.org/software/carmen http://software.incf.org/software/signalml multiplatform user-friendly display, annotation and analysis of EEG/MEG.. http://software.incf.org/software/signalml http://software.incf.org/software/neurotools NeuroTools is a collection of tools to support all tasks associated with a neural simulation project which are not handled by the simulation engine. http://software.incf.org/software/neurotools http://software.incf.org/software/cnslive LiveCD distribution for Computational Neuroscience Software.. http://software.incf.org/software/cnslive http://software.incf.org/software/stimfit A program for viewing and analyzing electrophysiological data.. http://software.incf.org/software/stimfit http://software.incf.org/software/incf-local-hub API and reference implementations of an INCF hub. http://software.incf.org/software/incf-local-hub http://software.incf.org/software/interactive-diagram-of-the-anatomical-connectivity-in-the-rat-hippocampal-formation-and-parahippocampal-region The interactive diagram provides a customizable display of all known anatomical connections between and within the hippocampal formation, parahippocampal and retrosplenial cortex region in the rat. http://software.incf.org/software/interactive-diagram-of-the-anatomical-connectivity-in-the-rat-hippocampal-formation-and-parahippocampal-region http://software.incf.org/software/neuropub-visualizer The NeuroPub Visualizer is your personal library of statistical parametric maps for functional and structural neuroimages on your iPad.. http://software.incf.org/software/neuropub-visualizer http://software.incf.org/software/ikaros Simulator for system-level brain models.. http://software.incf.org/software/ikaros http://software.incf.org/software/trakem2 Software for neural circuit reconstruction from LSM or EM image data sets. http://software.incf.org/software/trakem2 http://software.incf.org/software/stdpc StdpC is dynamic clamp software intended for the end-user neurophyiologist.. http://software.incf.org/software/stdpc http://software.incf.org/software/neuranim NeurAnim is a research aid for computational neuroscience.. http://software.incf.org/software/neuranim http://software.incf.org/software/isoitools The programs in this set of tools calculate isolation quality of clusters obtained from neural extracellular field / ensemble recordings using information-theoretic measures.. http://software.incf.org/software/isoitools http://software.incf.org/software/copy_of_loni-pipeline-environment The LONI Pipeline is a free workflow application primarily aimed at neuroimaging researchers.. http://software.incf.org/software/copy_of_loni-pipeline-environment http://software.incf.org/software/statistics-online-computational-resource-socr The Statistics Online Computational Resource (SOCR) provides portable online aids and computational libraries for probability and statistics education, technology based instruction and statistical computing.. http://software.incf.org/software/statistics-online-computational-resource-socr http://software.incf.org/software/lfpy LFPy is a Python module for simulations of extracellular field potentials.. http://software.incf.org/software/lfpy http://software.incf.org/software/trentool Trentool is a software for transfer entropy analysis in neural data. http://software.incf.org/software/trentool http://software.incf.org/software/neuroshare-matlab-library This is a matlab library for reading/writing Neuroshare (.nsn) files in Matlab.. http://software.incf.org/software/neuroshare-matlab-library http://software.incf.org/software/atlas3d Atlas3D is a multiplatform visualization tool which allows import, linear transformation, cutting and export of various data formats in 3D atlas space. http://software.incf.org/software/atlas3d http://software.incf.org/software/free-d 3D reconstruction, spatial normalization, and quantification of biological (e.g., neuroanatomical) structures from image stacks (histological, confocal, MRI, etc.). http://software.incf.org/software/free-d http://software.incf.org/software/pandora Database analysis and visualization of simulated and recorded electrophysiological data.. http://software.incf.org/software/pandora http://software.incf.org/software/modular-toolkit-for-data-processing-mdp Modular toolkit for Data Processing (MDP) is a Python data processing framework.. http://software.incf.org/software/modular-toolkit-for-data-processing-mdp http://software.incf.org/software/neurolex-wiki The NeuroLex project is a dynamic lexicon of neuroscience concepts. http://software.incf.org/software/neurolex-wiki http://software.incf.org/software/neuronvisio Neuronvisio is a Graphical User Interface for NEURON simulator enviroment.. http://software.incf.org/software/neuronvisio http://software.incf.org/software/xoonips XooNIps is a XOOPS-based infrastructure for the neuroinformatics platforms.. http://software.incf.org/software/xoonips http://software.incf.org/software/fiji Fiji is an image processing package based on ImageJ. http://software.incf.org/software/fiji http://software.incf.org/software/iqr iqr is a simulation software to graphically design and control large-scale neuronal models.. http://software.incf.org/software/iqr http://software.incf.org/software/spacan SpAcAn (Spontaneous Activity Analysis) is a collection of IGOR Pro functions for the detection and analysis of spontaneously occurring (non-triggered) events in electrophysiological recordings, such as spikes and synaptic currents and potentials. http://software.incf.org/software/spacan http://software.incf.org/software/slice-drop-1 Instantly view scientific and medical imaging data in 3D using your web browser. http://software.incf.org/software/slice-drop-1 http://software.incf.org/software/eeg-erp-portal EEG/ERP portal enables community researchers to store, update, download and search data and metadata from EEG/ERP experiments.. http://software.incf.org/software/eeg-erp-portal http://software.incf.org/software/synd SynD is an automated image analysis routine to analyze dendrite and synapse characteristics in immuno-fluorescence images. http://software.incf.org/software/synd http://software.incf.org/software/splitneuron SplitNeuron is a completely new approach to large-scale, biologically plausible, neural-network simulation.. http://software.incf.org/software/splitneuron http://software.incf.org/software/whole-brain-catalog-mobile Whole Brain Catalog Mobile is an image viewing engine for high resolution neuroscience data.. http://software.incf.org/software/whole-brain-catalog-mobile http://software.incf.org/software/sigtool sigTOOL provides a programming and analysis environment for processing electrophysiological data within MATLAB.. http://software.incf.org/software/sigtool http://software.incf.org/software/icsd-2d MATLAB scripts and a GUI tool for two-dimensional inverse current source density analysis. http://software.incf.org/software/icsd-2d http://software.incf.org/software/the-trees-toolbox A Matlab toolbox to generate, edit, visualize and analyze neuronal structure. http://software.incf.org/software/the-trees-toolbox http://software.incf.org/software/genn GeNN is a GPU enhanced Neuronal Network simulation environment based on code generation for NVidia CUDA. http://software.incf.org/software/genn http://software.incf.org/software/synapseem Program for analyzing electron microscopic (EM) images of synapses.. http://software.incf.org/software/synapseem http://software.incf.org/software/3d-brain-atlas-reconstructor 3d Brain Atlas Reconstructor (3dBAR, http://www.3dbar.org) allows reconstructing 3-D models of brain structures from 2-D delineations. http://software.incf.org/software/3d-brain-atlas-reconstructor http://software.incf.org/software/sinomo-singular-node-motifs This analysis-tool identifies singular node motifs in a network. http://software.incf.org/software/sinomo-singular-node-motifs http://software.incf.org/software/probability-distributome-project The Probability Distributome is an Interactive Web-based Resource for exploring and interrogating diverse Probability Distributions. http://software.incf.org/software/probability-distributome-project http://software.incf.org/software/neo Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. http://software.incf.org/software/neo http://software.incf.org/software/dae-tools A cross-platform equation-oriented process modelling and optimization software.. http://software.incf.org/software/dae-tools http://software.incf.org/software/spyke-viewer Spyke Viewer is a multi-platform GUI application for navigating, analyzing and visualizing electrophysiological datasets.. http://software.incf.org/software/spyke-viewer http://software.incf.org/software/kcsd The scripts implement the kCSD method described in the paper "Kernel Current Source Density Method" [Potworowski et al., Neural Computation (2012) 24, 541-575], for voltage data recorded using laminar (1D) or planar (2D) multielectrodes with arbitary distribution of contacts.. http://software.incf.org/software/kcsd http://software.incf.org/software/pynn A Python package for simulator-independent specification of neuronal network models. http://software.incf.org/software/pynn http://software.incf.org/software/neuroml NeuroML: a model description language for the computational neuroscience community.. http://software.incf.org/software/neuroml http://software.incf.org/software/moose-2 MOOSE is the Multiscale Object Oriented Simulation Environment for modeling and simulation in Neuroscience and Systems Biology.. http://software.incf.org/software/moose-2 http://software.incf.org/software/nest Software for large-scale neuronal network simulations.. http://software.incf.org/software/nest http://software.incf.org/software/waxholm-space Waxholm Space is a coordinate-based reference space for the mapping and registration of neuroanatomical data in the mouse brain.. http://software.incf.org/software/waxholm-space http://software.incf.org/software/ted Time Encoding and Decoding Toolbox.. http://software.incf.org/software/ted http://software.incf.org/software/scalable-brain-atlas The Scalable Brain Atlas (SBA) is a web-based interactive brain atlas which provides instant access to atlas templates of various species.. http://software.incf.org/software/scalable-brain-atlas http://software.incf.org/software/sumatra Sumatra is a tool for managing and tracking projects based on numerical simulation and/or analysis, with the aim of supporting reproducible research.. http://software.incf.org/software/sumatra http://software.incf.org/software/csa This is a demonstration implementation in Python of the Connection-Set Algebra (Djurfeldt, 2012).. http://software.incf.org/software/csa http://software.incf.org/software/incfdai Python API for the INCF Digital Atlasing infrastructure.. http://software.incf.org/software/incfdai http://software.incf.org/software/atlas3d-tool Research on 3d brain structures.. http://software.incf.org/software/atlas3d-tool http://software.incf.org/software/the-neurophysiological-biomarker-toolbox-nbt The Neurophysiological Biomarker Toolbox (NBT) is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers.. http://software.incf.org/software/the-neurophysiological-biomarker-toolbox-nbt http://software.incf.org/software/dbtransformer Tool for automatic transfer of relational database into semantic web resources.. http://software.incf.org/software/dbtransformer http://software.incf.org/software/erplab-toolbox ERPLAB Toolbox is a set of open source, freely available Matlab routines for analyzing ERP data.. http://software.incf.org/software/erplab-toolbox http://software.incf.org/software/incf-cloud-app A bundle including iRODS, Web Image Browser, INCF DAI API, Whole Brain Catalog, and much more. http://software.incf.org/software/incf-cloud-app http://software.incf.org/software/incf-neuron-registry INCF internal project for developing and managing the user interface for the neuron registry.. http://software.incf.org/software/incf-neuron-registry http://software.incf.org/software/mexi MEXI, MUSIC EXternal Interface, is a generic interface making MUSIC-enabled applications running on super-computers capable of communicating with the outside world. http://software.incf.org/software/mexi http://software.incf.org/software/neuart A neuroinformatics system for indexing neuroanatomical data using brain atlases.. http://software.incf.org/software/neuart http://software.incf.org/software/digital-brain Create a Publicly accessible signature over different channels.. http://software.incf.org/software/digital-brain http://software.incf.org/software/visn Visn software.. http://software.incf.org/software/visn http://software.incf.org/software/libneurosim Generic support library for neuronal simulators.. http://software.incf.org/software/libneurosim http://software.incf.org/software/axonal-beading-and-microtubule-quantification Interactive image analysis software for quantifying axonal beading morphology and focal microtubule loss using phase and fluorescent images a neuron. http://software.incf.org/software/axonal-beading-and-microtubule-quantification http://software.incf.org/software/nineml NineML: APIs and documentation.. http://software.incf.org/software/nineml http://software.incf.org/software/concierge Personal Database Software for Digital Research Resources.. http://software.incf.org/software/concierge http://software.incf.org/software/helmholtz A framework for creating neuroscience databases based on the Django web-development framework.. http://software.incf.org/software/helmholtz http://software.incf.org/software/information-breakdown-toolbox-ibtb The toolbox has several key features that make it useful to the neuroscience community and that will widen the domain of application of information theory to neuro- science. http://software.incf.org/software/information-breakdown-toolbox-ibtb http://software.incf.org/software/done-detection-of-outlier-neurons This tool implements a morphology-based approach for the automatic identification of outlier neurons. http://software.incf.org/software/done-detection-of-outlier-neurons http://software.incf.org/software/absorb-for-groupwise-registration This software package implements ABSORB: Atlas Building by Self-Organized Registration and Bundling – an algorithm for effective groupwise registration, which has been published as: Hongjun Jia, Guorong Wu, Qian Wang, Dinggang Shen, "ABSORB: Atlas Building by Self-Organized Registration and Bundling", NeuroImage, Vol.. http://software.incf.org/software/absorb-for-groupwise-registration http://software.incf.org/software/1000-functional-connectomes-project ATTENTION: The 1000 Functional Connectomes Project has a new home page at NITRC.. http://software.incf.org/software/1000-functional-connectomes-project http://software.incf.org/software/meg-tools MEG Localization using FOCUSS and MR-FOCUSS.. http://software.incf.org/software/meg-tools http://software.incf.org/software/brainscortex This suite of tools will generate the cortical surface of the brain.. http://software.incf.org/software/brainscortex http://software.incf.org/software/afni AFNI is a set of C programs for processing, analyzing, and displaying FMRI data.. http://software.incf.org/software/afni http://software.incf.org/software/fieldtrip FieldTrip is a Matlab software toolbox for MEG and EEG analysis that is being developed at the Centre for Cognitive Neuroimaging of the Donders Institute for Brain, Cognition and Behaviour in Nijmegen, The Netherlands, together with collaborating institutes.. http://software.incf.org/software/fieldtrip http://software.incf.org/software/braincsi BrainCSI is a tool for partial volume correction in CSI data.. http://software.incf.org/software/braincsi http://software.incf.org/software/nipy-diffusion-imaging-analysis DiPy is a python package for analyzing diffusion data. http://software.incf.org/software/nipy-diffusion-imaging-analysis http://software.incf.org/software/stochastic-tractography-system Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.. http://software.incf.org/software/stochastic-tractography-system http://software.incf.org/software/mpscope MPScope is a comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform.. http://software.incf.org/software/mpscope http://software.incf.org/software/diffusion-warp This project contains tools appropriate for the registration of diffusion tensor images to an average coordinate system.. http://software.incf.org/software/diffusion-warp http://software.incf.org/software/caret Caret is free, open source software used to visualize and analyze the structural and functional characteristics of cerebral and cerebellar cortex in humans, nonhuman primates, and rodents.. http://software.incf.org/software/caret http://software.incf.org/software/fmripower A common question investigators ask statisticians when working on grants is how to calculate power.. http://software.incf.org/software/fmripower http://software.incf.org/software/surfstat SurfStat is a Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory. http://software.incf.org/software/surfstat http://software.incf.org/software/fsl-extensions FSL extensions is a reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL). http://software.incf.org/software/fsl-extensions http://software.incf.org/software/lddmm LDDMM assigns a metric distances on the space of anatomical images.. http://software.incf.org/software/lddmm http://software.incf.org/software/fusion-ica-toolbox-fit FIT is a MATLAB toolbox which uses Independent Component Analysis (ICA) to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. http://software.incf.org/software/fusion-ica-toolbox-fit http://software.incf.org/software/unc-human-brain-atlas 3 human brain atlases have been created at UNC-Chapel Hill: a pediatric, an adult and an elderly one.. http://software.incf.org/software/unc-human-brain-atlas http://software.incf.org/software/qcqp Quadratically constrained quadratic programing (QCQP) technique in medical image analysis.. http://software.incf.org/software/qcqp http://software.incf.org/software/fmristat A Matlab toolbox for the statistical analysis of fMRI data. http://software.incf.org/software/fmristat http://software.incf.org/software/nice-sign NICE-SIGN is a nice sign of bias field correction (nonuniformity) in medical images.. http://software.incf.org/software/nice-sign http://software.incf.org/software/nutmeg NUTMEG (Neurodynamic Utility Toolbox for Magnetoencephalography) is an open-source MATLAB toolbox for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. http://software.incf.org/software/nutmeg http://software.incf.org/software/neuroanatomical-labeling-methods This NITRC Resource was created to host descriptions of protocols, definitions, and "rules of thumb" for the reliable identification and localization of neuroanatomical regions of interest and discussions of best practices in brain labeling.. http://software.incf.org/software/neuroanatomical-labeling-methods http://software.incf.org/software/cytoseg The goal of the Cytoseg project is to produce tools for automatic segmentation of of 3D electron microscopy, specifically neuropil.. http://software.incf.org/software/cytoseg http://software.incf.org/software/vmtk-in-3d-slicer This project provides a series of modules which enable functions of the Vascular Modeling Toolkit (http://www.vmtk.org) in 3D Slicer (http://www.slicer.org).. http://software.incf.org/software/vmtk-in-3d-slicer http://software.incf.org/software/cmrep The continuous medial representation (cm-rep) is a set of deformable modeling algorithms for shape analysis and structure-specific normalization.. http://software.incf.org/software/cmrep http://software.incf.org/software/jim Jim is a medical image display package that allows easy viewing and analysis of Magnetic Resonance, x-ray CT and other types of medical image.. http://software.incf.org/software/jim http://software.incf.org/software/seg3d Seg3D is a free volume processing sgementing tool that combines a flexible manual interface with powerful image processing and segmentation algorithms.. http://software.incf.org/software/seg3d http://software.incf.org/software/cocomac-paxinos3d-viewer CoCoMac-Paxinos3D viewer represents an interactive interface of macaque stereotaxic atlas with a connectivity database, allowing integrated data analysis and mapping between 3D structures with database vocabularies. http://software.incf.org/software/cocomac-paxinos3d-viewer http://software.incf.org/software/nc-igt-fast-imaging-library This software provides algorithms for the reconstruction of raw MR data.. http://software.incf.org/software/nc-igt-fast-imaging-library http://software.incf.org/software/artrepair-for-robust-fmri ArtRepair is a toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects.. http://software.incf.org/software/artrepair-for-robust-fmri http://software.incf.org/software/spatial-analysis-3d Spatial Analysis 3D is a user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns.. http://software.incf.org/software/spatial-analysis-3d http://software.incf.org/software/medinria MedINRIA allows to process and analyze a wide range of magnetic resonance (MR) images including anatomical MRI, functional MRI (fMRI), and diffusion tensor MRI (DT-MRI).. http://software.incf.org/software/medinria http://software.incf.org/software/connectomeviewer ConnectomeViewer is free, open source, cross-platform Python-based software application for visualization and analysis in connectome research.. http://software.incf.org/software/connectomeviewer http://software.incf.org/software/imagevis3d ImageVis3D is a new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC).. http://software.incf.org/software/imagevis3d http://software.incf.org/software/level-set-segmentation-for-slicer3 The modules in the framework support different tasks in the segmentation realization in 3DSlicer.. http://software.incf.org/software/level-set-segmentation-for-slicer3 http://software.incf.org/software/nipy-file-io NiBabel is a Python package for reading and writing a variety of medical and neuroimaging file formats.. http://software.incf.org/software/nipy-file-io http://software.incf.org/software/pymvpa PyMVPA is a Python package intended to ease statistical learning analyses of large datasets.. http://software.incf.org/software/pymvpa http://software.incf.org/software/brainsmush Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask.. http://software.incf.org/software/brainsmush http://software.incf.org/software/sharetools The ShapeTools library is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values.. http://software.incf.org/software/sharetools http://software.incf.org/software/tapir TAPIR (Tools for Advanced Parameterized Image Registration) is a set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems). http://software.incf.org/software/tapir http://software.incf.org/software/non-rigid-groupwise-registration-method The goal of the project is to provide an open source implementation of a non-rigid groupwise registration method.. http://software.incf.org/software/non-rigid-groupwise-registration-method http://software.incf.org/software/pynifti The PyNIfTI module is a Python interface to the NIfTI I/O libraries.. http://software.incf.org/software/pynifti http://software.incf.org/software/medical-image-visualization-and-analysis The MIVA software package (Medical Image Visualization and Analysis) is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously.. http://software.incf.org/software/medical-image-visualization-and-analysis http://software.incf.org/software/anatomist Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects.. http://software.incf.org/software/anatomist http://software.incf.org/software/mindseer MindSeer is a cross-platform application for 3D brain visualization.. http://software.incf.org/software/mindseer http://software.incf.org/software/marsbar-region-of-interest-toolbox MarsBaR (MARSeille Boîte À Région d'Intérêt) is a toolbox for SPM which provides routines for region of interest analysis.. http://software.incf.org/software/marsbar-region-of-interest-toolbox http://software.incf.org/software/multi-fiber-reconstruction-from-dw-mri This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data.. http://software.incf.org/software/multi-fiber-reconstruction-from-dw-mri http://software.incf.org/software/dinifti Convert DICOM images to NIfTI format. http://software.incf.org/software/dinifti http://software.incf.org/software/cleave CLEAVE is a UNIX-style command-line program which quickly computes multifactorial ANOVAs for large very data sets with minimal memory use (without loading all of the data into memory).. http://software.incf.org/software/cleave http://software.incf.org/software/mousebirn-atlasing-toolkit-mbat MBAT provides a workflow environment bringing together heterogenous, online biological image resources, a user’s image data and biological atlases in a concise, unified and intuitive workspace.. http://software.incf.org/software/mousebirn-atlasing-toolkit-mbat http://software.incf.org/software/brede-toolbox The Brede Toolbox is a package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl.. http://software.incf.org/software/brede-toolbox http://software.incf.org/software/brain-connectivity-toolbox The brain connectivity toolbox provides an easy access to a large selection of state of the art complex network measures, which characterize brain connectivity by easily computable and neurobiologically meaningful statistics, and are increasingly utilized in the description of large structural and functional connectivity datasets.. http://software.incf.org/software/brain-connectivity-toolbox http://software.incf.org/software/connectomewiki-knowledge-base ConnectomeWiki is a knowledge base for macro- and mesoscale brain region and brain connectivity information across species.. http://software.incf.org/software/connectomewiki-knowledge-base http://software.incf.org/software/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).. http://software.incf.org/software/advanced-normalization-tools http://software.incf.org/software/framework-for-open-programmatic-access The Framework for Open Programmatic Access (FOPA) aims to provide a standardized framework for communication and data exchange between medical imaging applications, with particular focus on neuroimaging technologies.. http://software.incf.org/software/framework-for-open-programmatic-access http://software.incf.org/software/asl-data-processing-tool-box This tool box is for arterial spin labeled perfusion MRI data processing.. http://software.incf.org/software/asl-data-processing-tool-box http://software.incf.org/software/scirun SCIRun is a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems.. http://software.incf.org/software/scirun http://software.incf.org/software/pipeline-neuroimaging-virtualenvironment The LONI Pipeline Neuroimaging Virtual Environment (PNVE), is a self-contained virtual machine that can be executed on a common laptop or desktop, enabling the Pipeline to run virtually anywhere.. http://software.incf.org/software/pipeline-neuroimaging-virtualenvironment http://software.incf.org/software/synchronized-histological-image-view-arc The Synchronized Histological Image Viewing Architecture (http://www.loni.ucla.edu/Software/SHIVA) is a Java-based visualization and analysis application.. http://software.incf.org/software/synchronized-histological-image-view-arc http://software.incf.org/software/analyze Analyze provides an integrated, comprehensive set of tools for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data.. http://software.incf.org/software/analyze http://software.incf.org/software/tortoise The TORTOISE software package is for processing diffusion MRI data.. http://software.incf.org/software/tortoise http://software.incf.org/software/parkinsons-disease-discovery-database Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources. http://software.incf.org/software/parkinsons-disease-discovery-database http://software.incf.org/software/shapeviewer The ShapeViewer (http://www.loni.ucla.edu/Software/ShapeViewer) is a simple, portable geometry viewer that supports the file formats used by CCB researchers and provides their most commonly needed viewing functions.. http://software.incf.org/software/shapeviewer http://software.incf.org/software/nipy-timeseries-analysis Nitime is a library for time-series analysis of data from neuroscience experiments.. http://software.incf.org/software/nipy-timeseries-analysis http://software.incf.org/software/loni-provenance-editor The LONI Provenance Editor (http://www.loni.ucla.edu/Software/ProvenanceEditor) is a self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information. http://software.incf.org/software/loni-provenance-editor http://software.incf.org/software/center-for-computational-biology-ccb The Center for Computational Biology (http://www.CCB.ucla.edu) provides 3 types of resources: * Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments).. http://software.incf.org/software/center-for-computational-biology-ccb http://software.incf.org/software/fast-fourier-transform-fft-javalibrary The FFT Java library (http://www.loni.ucla.edu/Software/FFT) is used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. http://software.incf.org/software/fast-fourier-transform-fft-javalibrary http://software.incf.org/software/multitracer MultiTracer (http://www.loni.ucla.edu/Software/MultiTracer) is a Java application that allows images to be displayed in three dimensions.. http://software.incf.org/software/multitracer http://software.incf.org/software/mri-digital-projection-system The MRI Digital Projection System uses Digital Light Processing® (DLP) technology that provides microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images.. http://software.incf.org/software/mri-digital-projection-system http://software.incf.org/software/bvqxtools BVQXtools is a Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab.. http://software.incf.org/software/bvqxtools http://software.incf.org/software/automated-image-registration-air The Automated Image Registration (AIR) tool is used for alignment of 3D and 2D images within and across subjects and across imaging modalities.. http://software.incf.org/software/automated-image-registration-air http://software.incf.org/software/scralyze SCRalyze is a powerful software for model-based analysis of peripheral psychophysiology (e.g.. http://software.incf.org/software/scralyze http://software.incf.org/software/camino-trackvis With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools.. http://software.incf.org/software/camino-trackvis http://software.incf.org/software/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. http://software.incf.org/software/freesurfer http://software.incf.org/software/nipy-community The purpose of NIPY is to make it easier to do better brain imaging research.. http://software.incf.org/software/nipy-community http://software.incf.org/software/gpu-based-affine-registration This tool can be used as a command line module with 3D Slicer (version 3 and above) for the affine registration of image volumes.. http://software.incf.org/software/gpu-based-affine-registration http://software.incf.org/software/sfmproject Structure from motion algorithms repository.. http://software.incf.org/software/sfmproject http://software.incf.org/software/nipy-pipeline-and-interfaces Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions.. http://software.incf.org/software/nipy-pipeline-and-interfaces http://software.incf.org/software/nipy-structural-and-functional-analysis Nipy aims to provide a complete Python environment for the analysis of structural and functional neuroimaging data.. http://software.incf.org/software/nipy-structural-and-functional-analysis http://software.incf.org/software/biomesh3d BioMesh3D is a free, easy to use program for generating quality meshes for use in biological simulations.. http://software.incf.org/software/biomesh3d http://software.incf.org/software/psychopy PsychoPy - Psychology software in Python.. http://software.incf.org/software/psychopy http://software.incf.org/software/map3d map3d supports interactive visualization of surface based time signals such as high resolution EEG, MEG, and ECG. http://software.incf.org/software/map3d http://software.incf.org/software/the-fmri-data-center A free database of fMRI data used in peer reviewed studies.. http://software.incf.org/software/the-fmri-data-center http://software.incf.org/software/template-image-processing-library Template Image Processing Library (TIPL) is a lightweight C++ template library designed mainly for medical imaging processing.. http://software.incf.org/software/template-image-processing-library http://software.incf.org/software/human-connectome-project-hcp *** THE HUMAN CONNECTOME PROJECT *** A multi-institutional project to map the white matter fiber pathways of the human brain using leading edge and advanced neuroimaging methods, genomics, cyto- and chemo-architectonics, and employing sophisticated multi-modal mathematical approaches, informatics, and interactive graphics visualization tools.. http://software.incf.org/software/human-connectome-project-hcp http://software.incf.org/software/v3d-and-v3d-neuron V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects.. http://software.incf.org/software/v3d-and-v3d-neuron http://software.incf.org/software/dtibrainscope This is a software package for processing diffusion tensor imaging data.. http://software.incf.org/software/dtibrainscope http://software.incf.org/software/bash4rfmri BASH Scripts for a resting-state functional MRI study.. http://software.incf.org/software/bash4rfmri http://software.incf.org/software/iso2mesh "Iso2mesh" is a Matlab/Octave-based mesh generation toolbox designed for easy creation of high quality surface and tetrahedral meshes from 3D volumetric images.. http://software.incf.org/software/iso2mesh http://software.incf.org/software/mesh-based-monte-carlo-mmc Mesh-based Monte Carlo, or MMC, is a Monte Carlo (MC) solver for photon migration in 3D turbid media.. http://software.incf.org/software/mesh-based-monte-carlo-mmc http://software.incf.org/software/monte-carlo-extreme-mcx Monte Carlo eXtreme, or MCX, is a Monte Carlo simulation software for photon migration in 3D turbid media.. http://software.incf.org/software/monte-carlo-extreme-mcx http://software.incf.org/software/monte-carlo-simulation-software-tmcimg tMCimg uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties.. http://software.incf.org/software/monte-carlo-simulation-software-tmcimg http://software.incf.org/software/the-cognitive-atlas The Cognitive Atlas (http://www.cognitiveatlas.org) is a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive neuroscience.. http://software.incf.org/software/the-cognitive-atlas http://software.incf.org/software/gestr GesTr is a cross platform, open source gesture tracking program.. http://software.incf.org/software/gestr http://software.incf.org/software/neuroimaging-data-access-group The NeuroImaging Data Access Group (NIDAG) is an informal working group, dedicated to improving access to neuroimaging results in a free and open-access manner.. http://software.incf.org/software/neuroimaging-data-access-group http://software.incf.org/software/probabilisticbiascorrection A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module. http://software.incf.org/software/probabilisticbiascorrection http://software.incf.org/software/vectorvaluedhistogramnormalizer Implement the methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf as and ITK filter. http://software.incf.org/software/vectorvaluedhistogramnormalizer http://software.incf.org/software/rapidart RapidArt provides software for detecting artifacts and performing individual region-of-interest (ROI) based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results. http://software.incf.org/software/rapidart http://software.incf.org/software/brainsfit A program for registering images with with mutual information based metric.. http://software.incf.org/software/brainsfit http://software.incf.org/software/rest-a-toolkit-for-resting-state-fmri REsting State fMRI data analysis Toolkit (REST) is a user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis.. http://software.incf.org/software/rest-a-toolkit-for-resting-state-fmri http://software.incf.org/software/spinesegmentation-module-for-3dslicer 3D Slicer module for automated segmentation of the spine.. http://software.incf.org/software/spinesegmentation-module-for-3dslicer http://software.incf.org/software/fluid-registration-and-atlas-toolkit FRAT provides c++ libraries and applications for performing fluid registration based operations on 2D and 3D images.. http://software.incf.org/software/fluid-registration-and-atlas-toolkit http://software.incf.org/software/brainscut BRAINSCut is a software package for segmentation of structures using automated neual networks.. http://software.incf.org/software/brainscut http://software.incf.org/software/brainsconstellationdetector This program will find the mid-sagittal plane, the AC, PC, and mpj points in an image, and create an AC/PC aligned data set with the AC point at the center of the voxel lattice (la beled at the origin of the image physical space.) This work is an extention of the algorithms originally described by Dr.. http://software.incf.org/software/brainsconstellationdetector http://software.incf.org/software/brainsroiauto Automatically creates a mask based on the 'foreground' of an anatomical scan volume. http://software.incf.org/software/brainsroiauto http://software.incf.org/software/dtiprocess-toolkit DTIProcess is a DTI processing and analysis toolkit developed in UNC and University of Utah.. http://software.incf.org/software/dtiprocess-toolkit http://software.incf.org/software/spanish-resting-state-network Spanish Resting State Network (SRSN); Foro para compartir datos y conocimiento sobre esta red.. http://software.incf.org/software/spanish-resting-state-network http://software.incf.org/software/the-neuro-bureau The Neuro Bureau is neuro-collaboration in action.. http://software.incf.org/software/the-neuro-bureau http://software.incf.org/software/best-practices-for-software-development "Best Practices for Software Development in the Imaging Community: Users and Developers Unite" is a tutorial that will take place as part of MICCAI 2010 is the 13th International Conference on Medical Image Computing and Computer Assisted Intervention, will be held from September 20-24, 2010 in Beijing, China.. http://software.incf.org/software/best-practices-for-software-development http://software.incf.org/software/mindboggle-automated-brain-labeling Mindboggle automates anatomical labeling of human brain MR data.. http://software.incf.org/software/mindboggle-automated-brain-labeling http://software.incf.org/software/r-package-for-adaptive-fmri-analysis The package fmri provides fMRI analysis with R using structural adaptive smoothing methods.. http://software.incf.org/software/r-package-for-adaptive-fmri-analysis http://software.incf.org/software/gambit GAMBIT(Groupwise Automatic Mesh Based analysis of cortIcal Thickness) is an end-to-end application developped at UNC-Chapel Hill allowing groupwise automatic mesh-based analysis of cortical thickness as well as other surface area measurements. http://software.incf.org/software/gambit http://software.incf.org/software/nptk NPTK provides non-rigid registration/distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI. http://software.incf.org/software/nptk http://software.incf.org/software/dfbidb DFBIdb is a suite of tools for efficient management of neuroimaging project data.. http://software.incf.org/software/dfbidb http://software.incf.org/software/miview MIview is an OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility.. http://software.incf.org/software/miview http://software.incf.org/software/brainvox Brainvox is an interactive 3D rendering and neuroanatomical analysis package developed for analyzing focal brain lesions and functional brain imaging data (Damasio and Frank, 1991; Frank, Damasio and Grabowski, 1997). http://software.incf.org/software/brainvox http://software.incf.org/software/brain-lesion-segmentation-tool-using-svm Brain lesions appear in different brain diseases as well as in normal aging; they can be due to small vessel disease, infarcts, MS, or other reasons.. http://software.incf.org/software/brain-lesion-segmentation-tool-using-svm http://software.incf.org/software/vervet-probabilistic-atlas The vervet (Chlorocebus pygerythrus) probabilistic atlas defines an anatomical space (template) with associated tissue and regional prior probability maps.. http://software.incf.org/software/vervet-probabilistic-atlas http://software.incf.org/software/diamond UC Davis IDeA Lab Applications for Management Of Neuroimaging Data - View dicom files and assemble them into 3D volumes.. http://software.incf.org/software/diamond http://software.incf.org/software/b0-and-eddy-current-correction-for-dti Software tool (excecutable and source code in C and C++) to correct distortions in diffusion MR images that are generated by main magnetic field inhomogeneities and eddy current induced fields generated from the direction-dependent diffusion encoding.. http://software.incf.org/software/b0-and-eddy-current-correction-for-dti http://software.incf.org/software/brainstracer BRAINSTracer - a graphical program to trace anatomical features in 3D image volumes.. http://software.incf.org/software/brainstracer http://software.incf.org/software/jip-fmri-analysis-toolkit The JIP Toolkit was developed primarily for analysis of rodent and non-human primate fMRI data.. http://software.incf.org/software/jip-fmri-analysis-toolkit http://software.incf.org/software/gamma GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data.. http://software.incf.org/software/gamma http://software.incf.org/software/pipeline-system-for-octave-and-matlab A pipeline is a collection of jobs, i.e.. http://software.incf.org/software/pipeline-system-for-octave-and-matlab http://software.incf.org/software/automatic-segmentation-tool-adapter More and more automatic segmentation tools are publicly available to today's researchers.. http://software.incf.org/software/automatic-segmentation-tool-adapter http://software.incf.org/software/segmentation-of-hippocampus-subfields A software package described in the upcoming NeuroImage paper "Nearly Automatic Segmentation of Hippocampal Subfields in In Vivo Focal T2-Weighted MRI" by Yushkevich et al.. http://software.incf.org/software/segmentation-of-hippocampus-subfields http://software.incf.org/software/nvm NVM is an open-source software tool for locating and measuring neuroanatomy in structural volumetric image data.. http://software.incf.org/software/nvm http://software.incf.org/software/brainimagejava BrainImageJava is a multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research.. http://software.incf.org/software/brainimagejava http://software.incf.org/software/dicom-browser DICOM Browser is a platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver.. http://software.incf.org/software/dicom-browser http://software.incf.org/software/slicer3-example-modules Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. http://software.incf.org/software/slicer3-example-modules http://software.incf.org/software/loni-debabeler The LONI Debabeler manages the conversion of imaging data from one file format and convention to another.. http://software.incf.org/software/loni-debabeler http://software.incf.org/software/loni-inspector The LONI Inspector is an application for examining medical image files.. http://software.incf.org/software/loni-inspector http://software.incf.org/software/3d-interactive-chemical-shift-imaging 3D Interactive Chemical Shift Imaging (3DiCSI) is a user-friendly and comprehensive software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis. http://software.incf.org/software/3d-interactive-chemical-shift-imaging http://software.incf.org/software/brainwaver Characterisation of small-world networks constructed from wavelet analysis of resting fMRI.. http://software.incf.org/software/brainwaver http://software.incf.org/software/landman-neuroimaging-tools Project to provide long-term hosting and release for small tools related to medical image analysis.. http://software.incf.org/software/landman-neuroimaging-tools http://software.incf.org/software/dti-fiber-tract-statistics This is a command line tool which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts.. http://software.incf.org/software/dti-fiber-tract-statistics http://software.incf.org/software/neurolens NeuroLens is an integrated environment for the analysis and visualization of functional neuroimages. http://software.incf.org/software/neurolens http://software.incf.org/software/xjview-a-viewing-tool-for-spm xjView is a viewing program for SPM2 and SPM5.. http://software.incf.org/software/xjview-a-viewing-tool-for-spm http://software.incf.org/software/brainsdemonwarp BrainDemonsWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms.. http://software.incf.org/software/brainsdemonwarp http://software.incf.org/software/brainstorm Brainstorm is a free Matlab application dedicated to MEG and EEG data visualization, processing and cortical source estimation.. http://software.incf.org/software/brainstorm http://software.incf.org/software/tractor-tractography-with-r The TractoR (Tractography with R) project includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only).. http://software.incf.org/software/tractor-tractography-with-r http://software.incf.org/software/quantitative-diffusion-tools The Quantitative Diffusion Tools provide Slicer3 modules for quantitative diffusion analysis.. http://software.incf.org/software/quantitative-diffusion-tools http://software.incf.org/software/camino Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. http://software.incf.org/software/camino http://software.incf.org/software/brainvoyager-viewer BrainVoyager Brain Viewer allows to browse and inspect essential BrainVoyager data files.. http://software.incf.org/software/brainvoyager-viewer http://software.incf.org/software/econnectome eConnectome (Electrophysiological Connectome) is an open-source MATLAB toolbox for imaging brain functional connectivity from electrophysiologic signals (http://econnectome.umn.edu/).. http://software.incf.org/software/econnectome http://software.incf.org/software/matlab-tutorial-on-diffusion-tensor-mri This is an on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing.. http://software.incf.org/software/matlab-tutorial-on-diffusion-tensor-mri http://software.incf.org/software/spharm-mat SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.. http://software.incf.org/software/spharm-mat http://software.incf.org/software/subject-order-independent-group-ica While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results.. http://software.incf.org/software/subject-order-independent-group-ica http://software.incf.org/software/nyu-csc-testretest The NYU CSC TestRetest resource includes EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants.. http://software.incf.org/software/nyu-csc-testretest http://software.incf.org/software/brainvoyager-brain-tutor The free BrainVoyager Brain Tutor teaches you knowledge about the human brain through interactive exploration of rotatable 3D models.. http://software.incf.org/software/brainvoyager-brain-tutor http://software.incf.org/software/dti-toolkit-dti-tk DTI-TK is a spatial normalization & atlas construction toolkit, designed from ground up to support the manipulation of diffusion-tensor images (DTI) with special cares taken to respect the tensorial nature of the data.. http://software.incf.org/software/dti-toolkit-dti-tk http://software.incf.org/software/rex REX is a stand-alone MATLAB-based toolkit for the rapid and flexible exploration of ROI response waveforms and other signals from across large fMRI datasets.. http://software.incf.org/software/rex http://software.incf.org/software/loni-de-identification-debablet The LONI de-identification Debablet is an application for removing patient-identifying information from medical image files.. http://software.incf.org/software/loni-de-identification-debablet http://software.incf.org/software/brainfx A developer tool to provide batch processing capability for pipelines.. http://software.incf.org/software/brainfx http://software.incf.org/software/snpm The Statistical nonParametric Mapping toolbox provides an extensible framework for voxel level non-parametric permutation/randomisation tests of functional Neuroimaging experiments with independent observations. http://software.incf.org/software/snpm http://software.incf.org/software/brainmap-database BrainMap is a community database of published functional neuroimaging studies (mainly PET and fMRI).. http://software.incf.org/software/brainmap-database http://software.incf.org/software/fsl FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data.. http://software.incf.org/software/fsl http://software.incf.org/software/bioimage-suite BioImage Suite is a general purpose registration/segmentation/visualization suite.. http://software.incf.org/software/bioimage-suite http://software.incf.org/software/slicer3-module-rician-noise-filter Two Slicer3 modules removing rician noise in diffusion tensor MRI.. http://software.incf.org/software/slicer3-module-rician-noise-filter http://software.incf.org/software/gtract GTRACT is a Diffusion Tensor fiber tracking suite that includes streamline tracking tools.. http://software.incf.org/software/gtract http://software.incf.org/software/mrtrix 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. http://software.incf.org/software/mrtrix http://software.incf.org/software/hammer-deformable-registration The HAMMER package performs high-dimensional warping of brain images.. http://software.incf.org/software/hammer-deformable-registration http://software.incf.org/software/camba Software respository containing pipelines of chained modules and GUI for batch processing.. http://software.incf.org/software/camba http://software.incf.org/software/gradient-non-linearity-unwarping-tool The Brain Morphometry testbed of the BIRN provides a tool to correct gradient non-linearity distortions in MR structural images.. http://software.incf.org/software/gradient-non-linearity-unwarping-tool http://software.incf.org/software/fiv The Functional Image Viewer, also known as FIV, is a tool for visualizing functional and anatomic MRI data. http://software.incf.org/software/fiv http://software.incf.org/software/arctic ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness.. http://software.incf.org/software/arctic http://software.incf.org/software/fmri-cpca Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework.. http://software.incf.org/software/fmri-cpca http://software.incf.org/software/mango Mango is a medical image viewer for Windows, Mac OS X, Unix, Linux, and Web platforms.. http://software.incf.org/software/mango http://software.incf.org/software/brainvisa-morphology-extensions An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging.. http://software.incf.org/software/brainvisa-morphology-extensions http://software.incf.org/software/3dslicerlupuslesionmodule The purpose of this Slicer3 module is to provide a capability for performing white matter lesion classification and summary. http://software.incf.org/software/3dslicerlupuslesionmodule http://software.incf.org/software/mipav The MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. http://software.incf.org/software/mipav http://software.incf.org/software/artifact-detection-tools-art Toolbox for post-processing fMRI data.. http://software.incf.org/software/artifact-detection-tools-art http://software.incf.org/software/mri-studio MRI and DTI imaging software tool. http://software.incf.org/software/mri-studio http://software.incf.org/software/voxbo VoxBo is a highly modular and interoperable collection of free tools for brain image manipulation and analysis, focusing on fMRI and lesion analysis.. http://software.incf.org/software/voxbo http://software.incf.org/software/hi-speed-software-packets HI-SPEED Software Packets contain (1) unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques, (2) 2-dimensional and 3-dimensional analytical (Shepp-Logan) magnetic resonance imaging phantoms in both the Fourier and image domains, (3) techniques for reporting the underlying signal-to-noise ratio in magnetic resonance (MR) images, (4) Probabilistic Identification and EStimation of NOise (PIESNO)---a technique for identifying noise-only pixels and estimating the underlying noise standard deviation in MR images, and (5) a signal-transformational technique for breaking the noise floor in MR images.. http://software.incf.org/software/hi-speed-software-packets http://software.incf.org/software/idea-lab-brain-image-processing-suite Suite of tools for brain image analysis.. http://software.incf.org/software/idea-lab-brain-image-processing-suite http://software.incf.org/software/vamca-cortical-meta-analysis-toolbox VAMCA: Visualization And Meta-analysis on Cortical Anatomy is a stand-alone, open source human cortical meta-analysis and visualization toolbox for MatLab.. http://software.incf.org/software/vamca-cortical-meta-analysis-toolbox http://software.incf.org/software/fbirn-image-processing-scripts-fips FBIRN Imaging Processing Scripts (FIPS) is a FSL package for the comprehensive management of large-scale multi-site fMRI projects, including data storage, retrieval, calibration, analysis, multi-modal integration, and quality control. http://software.incf.org/software/fbirn-image-processing-scripts-fips http://software.incf.org/software/svv This project is a simple Surface and Volumetric Visualization application that has been designed to facilitate rapid and flexible visualization from neuroanatomically segmented results. http://software.incf.org/software/svv http://software.incf.org/software/talairach-daemon The Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach atlas. http://software.incf.org/software/talairach-daemon http://software.incf.org/software/automatic-registration-toolbox Automatic detection of the AC and PC landmarks on 3D structural MRI scans.. http://software.incf.org/software/automatic-registration-toolbox http://software.incf.org/software/dw-mri-random-walk-simulator The DW-MRI Random Walk Simulator provides a simple interface to simulate Brownian motion in arbitrary, complex environments.. http://software.incf.org/software/dw-mri-random-walk-simulator http://software.incf.org/software/segmentation-validation-engine The Segmentation Validation Engine (SVE) provides an automated online framework for performing validation studies of skull-stripping methods.. http://software.incf.org/software/segmentation-validation-engine http://software.incf.org/software/brainmask-volume-processing-tool Segmentation of the brain from three-dimensional MR images is a crucial pre-processing step in morphological and volumetric brain studies.. http://software.incf.org/software/brainmask-volume-processing-tool http://software.incf.org/software/3d-slicer An extensible, cross-platform, totally open research platform for image computing. http://software.incf.org/software/3d-slicer http://software.incf.org/software/hammer-and-wml-modules-for-3d-slicer HAMMER is the acronym for Hierarchical Attribute Matching Mechanism for Elastic Registration (Dinggang Shen, Christos Davatzikos, HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration, IEEE Trans.. http://software.incf.org/software/hammer-and-wml-modules-for-3d-slicer http://software.incf.org/software/r-package-for-adaptive-dwi-analysis The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model.. http://software.incf.org/software/r-package-for-adaptive-dwi-analysis http://software.incf.org/software/candi-neuroimaging-access-point The Child and Adolescent NeuroDevelopment Initiative (CANDI at UMass Medical School is making available a series of structural brain images, as well as their anatomic segmentations, demographic and behavioral data and a set of related morphometric resources. http://software.incf.org/software/candi-neuroimaging-access-point http://software.incf.org/software/jist-resources-for-algorithm-development This repository stores plugins, tutorial code, and examples demonstrating MRI manipulation within the MIPAV plugin environment.. http://software.incf.org/software/jist-resources-for-algorithm-development http://software.incf.org/software/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.. http://software.incf.org/software/loni-pipeline-environment http://software.incf.org/software/valmap-simple-statistical-mapping-tool valmap is a command line voxel-wise statistical analysis program for images.. http://software.incf.org/software/valmap-simple-statistical-mapping-tool http://software.incf.org/software/staple STAPLE is an algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations.. http://software.incf.org/software/staple http://software.incf.org/software/jist-java-image-science-toolkit Java Image Science Toolkit (JIST) provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm.. http://software.incf.org/software/jist-java-image-science-toolkit http://software.incf.org/software/brainvisa BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research.. http://software.incf.org/software/brainvisa http://software.incf.org/software/brainscape Brainscape is a database for resting state functional connectivity studies.. http://software.incf.org/software/brainscape http://software.incf.org/software/mri-defacer Tool to remove facial features from an MRI structural image for the purpose of de-identification. http://software.incf.org/software/mri-defacer http://software.incf.org/software/web-game-for-collaborative-labeling Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system.. http://software.incf.org/software/web-game-for-collaborative-labeling http://software.incf.org/software/brainsolution BrainSolution is a collection of tools for MRI T1 brain image segmentation in the Windows® environment.. http://software.incf.org/software/brainsolution http://software.incf.org/software/toads-cruise-brain-segmentation-tools The TOADS-CRUISE Brain Segmentation Tools are a collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images.. http://software.incf.org/software/toads-cruise-brain-segmentation-tools http://software.incf.org/software/itk-snap ITK-SNAP is an open-source software application for medical image segmentation.. http://software.incf.org/software/itk-snap http://software.incf.org/software/abc-atlas-based-classification ABC (Atlas Based Classification) is a full segmentation pipeline developed and used at University of North Carolina and University of Utah for brain MRIs.. http://software.incf.org/software/abc-atlas-based-classification http://software.incf.org/software/brainparser Brain Parser software uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes.. http://software.incf.org/software/brainparser http://software.incf.org/software/brainvoyager-qx BrainVoyager QX is a powerful neuroimaging software package.. http://software.incf.org/software/brainvoyager-qx http://software.incf.org/software/brains The BRAINS (Brain Research: Analysis of Images, Networks, and Systems) image analysis software has been developed to study the brain thus providing a better understand of psychiatric and neurological disorders. http://software.incf.org/software/brains http://software.incf.org/software/spm The SPM software package has been designed for the analysis of brain imaging data sequences.. http://software.incf.org/software/spm http://software.incf.org/software/spharm-pdm-unc-toolbox Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.. http://software.incf.org/software/spharm-pdm-unc-toolbox http://software.incf.org/software/generalized-covariance-analysis-gcva Generalized Covariance Analysis: a platform for any PCA-based analysis on functional neuroimaging data (PET and fMRI).. http://software.incf.org/software/generalized-covariance-analysis-gcva http://software.incf.org/software/multi-modal-mri-reproducibility-resource We have acquired scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease).. http://software.incf.org/software/multi-modal-mri-reproducibility-resource http://software.incf.org/software/numerical-fibre-generator-nfg NFG is a collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them.. http://software.incf.org/software/numerical-fibre-generator-nfg http://software.incf.org/software/xnat XNAT is an open source imaging informatics platform designed to facilitate management and exploration of medical imaging and related data.. http://software.incf.org/software/xnat http://software.incf.org/software/mricron MRIcron is a cross-platform NIfTI format image viewer.. http://software.incf.org/software/mricron http://software.incf.org/software/neurodebian This is a collaborative effort to package neuroscience-related software for the Debian operating system.. http://software.incf.org/software/neurodebian http://software.incf.org/software/group-ica-toolbox-gift-and-eegift Group ICA Toolbox is a MATLAB toolbox which implements multiple algorithms for independent component analysis of group magneto resonance imaging data (GIFT) and electro encephalogram data (EEGIFT) to group studies. http://software.incf.org/software/group-ica-toolbox-gift-and-eegift http://software.incf.org/software/computational-morphometry-toolkit-cmtk A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O.. http://software.incf.org/software/computational-morphometry-toolkit-cmtk http://software.incf.org/software/dsi-studio DSI Studio is a software for diffusion MR images analysis.. http://software.incf.org/software/dsi-studio http://software.incf.org/software/neuron .. http://software.incf.org/software/neuron