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197 matching tools found


* Entries marked with an asterisk have been added to the Tools Registry by the database maintainers in their desire for completeness. As a result, the listings for these tools should be considered incomplete. We would love to have all entries maintained by software authors and maintainers; please contact us at cma-www@cma.mgh.harvard.edu if you see your work listed here and would like to have an up to date listing.

indicates tools supported by The Human Brain Project.
indicates tools that support NIfTI-1.


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3D Slicer (MIT AI Lab; Surgical Planning Lab, Brigham and Women's Hospital)
3DViewnix (The University of Pennsylvania)
ACTIV 2000 (Neuroradiology Dpt, C.H.U. de Bicêtre)
AFNI
AIR 5.0 (Automated Image Registration)
AMIDE (Amide's a Medical Image Data Examiner)
Amira* (Visual Concepts GmbH)
analySIS® (Soft Imaging System)
Analyze* (Mayo Clinic)
Anatomist (Neurospin, I2BM, CEA)
AngioCalc (Cerebral Aneurysm Calculator)
arivis Vision4D (arivis AG, Germany) (arivis AG)
Atrophy Simulation Package (SBIA Radiology, University of Pennsylvania)
Autoaligner (Bitplane Inc.)
b3d (Center for Neuroscience, University of California, Davis)
BAMM (University of Cambridge, King's College London and the Wellcome Trust)
bioelectromagnetism (matlab tools for eeg/meg/mri)
BIRN Human Imaging Database (HID) (Biomedical Informatics Research Network)
Blox (Kennedy Krieger Institute & Johns Hopkins Hospital)
Brain Atlas for Functional Imaging (Theime Medical Publishers)
BrainGraph Editor 1.0 Beta (The BrainGraph Editor 1.0 Beta is a JAVA application designed to create taxonomies or hierarchies.)
Brain Image (Stanford Psychiatry Neuroimaging Laboratory)
BrainInfo (University of Washington, Seattle)
BrainMagix (Imagilys)
BrainMaps.org (High-Resolution Brain Maps and Brain Atlases)
BRAINS (Brain Research: Analysis of Images, Networks, and Systems) (Iowa Mental Helath Clinical Research Center)
BrainStorm (University of Southern California; CNRS LENA Paris; Los Alamos National Lab.)
BrainVISA (IFR 49 Paris/I2BM CEA)
BrainVoyager (Brain Innovation B.V.)
Brede Toolbox (IMM, Techical University of Denmark)
btrack (National Center for Microscopy and Imaging Research)
BYU2Vox (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
Camino (Department of Computer Science, University College London)
cardviews (Center for Morphometric Analysis, Massachusetts General Hospital)
CARET (Washington University in St. Louis School of Medicine)
CATNAP (Johns Hopkins University School of Medicine)
CellProfiler cell image analysis software (Broad Institute of Harvard and MIT)
COMKAT: Compartment Model Kinetic Analysis Tool (University Hospitals of Cleveland)
Conexus (Center for Neuroscience, University of California Davis)
Corner_Cube (University of Minnesota)
DC Harvester* (fMRI Data Center, Dartmouth College)
DCMTK (OFFIS DICOM Toolkit)
DCSearch (fMRI Data Center, Dartmouth College)
DCViewer (fMRI Data Center, Dartmouth College)
Dend (National Center for Microscopy and Imaging Research)
Diatrack 3.03 (Semasopht)
DICOMscope (DICOM Viewer)
DicomWorks (Universities of Lille and Lyon, France)
diffusion_smoothing_tool (Draper Lab & MGH)
diffusion TENSOR Visualizer (Image Computing & Analysis Lab., Radiology, The Univ. of Tokyo Hospital)
DPTools (Neuroradiology Dpt, C.H.U. de Bicêtre)
DTI Gradient Table Creator (F.M. Kirby Research Center, Kennedy Krieger Institute, Johns Hopkins University)
DtiStudio (Laboratory of Brain Anatomical MRI, Johns Hopkins Radiology)
DTI Track 2005 (INRIA Sophia Antipolis, France)
Edgewarp3D* (The University of Michigan/Visible Human Project)
EM3D (Uel J. McMahan Laboratory, Stanford University, Dept. of Neurobiology, Dept. of Structural Biology)
EMS (Expectation-Maximization Segmentation) (Medical Image Computing, Leuven, Belgium)
EvIdent(r) (National Research Council, Institute for Biodiagnostics)
ezDICOM (University of Nottingham)
FACT (Interdisciplinary MRI/MRS Lab, National Taiwan University)
FIASCO (Functional Image Analysis Software Computational Olio) (CMU Statistics Department)
Fiber Tracking (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
Fiber Viewer (UNC at Chapel Hill, Psychiatry and computer sciences departments)
Fido (National Center for Microscopy and Imaging Research)
FilamentTracer (Bitplane Inc.)
FisWidgets (University of Pittsburgh)
fMRIstat (Montreal Neurological Institute )
form*Z* (auto*des*sys)
Free-D (INRA, France)
FreeSurfer (NMR Center, Massachusetts General Hospital)
FSL - The FMRIB Software Library (FMRIB, Oxford University)
geWorkbench (Center for Computational Biology and Bioinformatics, Columbia University)
Gimp* (Peter Mattis and Spencer Kimball)
gpetview (Gtk-base Analyze image viewer)
Gradient non-linearity distortion correction (Martinos Center, MGH, Boston)
Group ICA Toolbox (GIFT and EEGIFT) (The MIND Research Network)
HAMMER (SBIA, Department of Radiology, Upenn )
Head Circumference (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
IHCorr (IDeA Lab, Center for Neuroscience, UC Davis)
iiV (internet image Viewer) (Cognitive Neuroimaging Unit, VA Medical Center, University of Minnesota, Minneapolis)
ImageJ (Research Services Branch, NIMH)
ImageMagick* (ImageMagick Studio LLC)
Image-Pro Plus 5.0 (Media Cybernetics, Inc.)
ImageTrak (Fluorescence image visualization and analysis for Macintosh OS X)
Imaris (Bitplane Inc.)
ImarisColoc (Bitplane Inc.)
Imaris InPress (Bitplane Inc.)
ImarisMeasurementPro (Bitplane Inc.)
ImarisTrack (Bitplane Inc.)
ImarisXT (Bitplane Inc.)
Imconverter (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
Imread (University of Colorado Health Sciences Center)
InsightSNAP (Penn Image Computing and Science Lab, University of Pennsylvania, CS dept UNC Chapel Hill)
Intensity Rescaler (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
Intramodal registration
IrfanView (by Irfan Skiljan)
ISI-Distance - Measure for Spike Train Synchrony (Institute for Nonlinear Science, University of California San Diego)
ITK (Insight Segmentation and Registration Toolkit)
JDTI (Duke University Medical Center)
Jim (Xinapse Systems)
JIV (Java Image Viewer) (A 3D Image Data Visualization and Comparison Tool)
JViewer (A Java-based 2D and 3D image viewer)
L-Measure (Krasnow Institute, George Mason university)
L-Neuron (Krasnow Institute, George Mason University)
LONI Debabeler (The LONI Debabeler manages the conversion of imaging data between multiple file fomats)
LONI De-Identification Debablet (The LONI Debablet de-identifies medical image files.)
LONI ICE (Generates seed points for image processing applications)
LONI Inspector (The LONI Inspector is an application for displaying, searching, comparing, and exporting metadata.)
LONI Pipeline (Laboratory of Neuro Imaging, UCLA)
LONI Visualization Environment (LOVE)
LORETA (low resolution brain electromagnetic tomography) (The KEY Institute for Brain-Mind Research, University Hospital of Psychiatry, Zurich, Switzerland)
Lyngby (Matlab functional neuroimaging analysis toolbox)
Mango (Research Imaging Institute, UTHSC San Antonio)
match-colors (Center for Neuroscience, University of California, Davis)
MATITK (Call ITK from MATLAB)
MedINRIA (Asclepios Research Team, INRIA Sophia Antipolis, France)
MEDx* (Sensor Systems, Inc.)
MeVisLab* (MeVis)
MINC - core (Medical Image NetCDF)
MINC - EMMA (A MATLAB interface for MINC)
MINC - mni_autoreg (A highly customisable Linear and Non-Linear registration Package)
MINC - N3 (An automated tool for correction of intensity nonuniformity in MRI data)
MINC - volume_io (A simplified API for the MINC file format)
MIPAV (Medical Image Processing, Analysis and Visualization - NIH)
MIView (gbooksoft.com)
MOUSE BIRN ATLASING TOOLKIT (MBAT) 2.0 Beta (This is a collaborative effort of six laboratories. See other information section below for detail.)
Mouse Brain Atlas Web References (The Mouse Brain Library)
mri3dX* (Aston University School of Life and Health Science)
MRIcro (University of South Carolina)
mri_toolbox (matlab functions for Analyze 7.5)
MRIVIEW (Biophysics Group (P-21), Los Alamos National Laboratory )
MRI Watcher (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
NeuroLens (A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital)
Neurolucida (System for neuron tracing, brain mapping and neuroImaging)
NeuronMetrics (Developmental Neurogenetics Laboratory, University of Arizona)
NeuroServ (The MITRE Corporation)
NeuroTerrain Atlas Server (Laboratory for Bioimaging & Anatomical Informatics, Dept. Neurobio. & Anat., Drexel U. Coll. of Med.)
NeuroTerrain NetOStat Atlas Browser (+ NT-SDK) (Laboratory for Bioimaging & Anatomical Informatics, Dept. Neurobio. & Anat., Drexel U. Coll. of Med.)
NIH Image (Research Services Branch, NIMH)
NIS (NeuroImaging Statistics) (University of Pittsburgh)
Non-linear normalization of MRI brain scans
Northern Eclipse 6.0
NPAIRS (University of Minnesota)
NVM (Neuromorphometrics)
Olfactory Glomerular Response Mapping (University of California, Irvine)
OsiriX
Partial Least Squares GUI for PET, fMRI & EEG/MEG (Rotman Res Inst - Baycrest Centre, Univ of Toronto)
PMOD (PMOD Technologies)
PV-Wave* (Visual Numerics)
RAVENS (Regional volumetric analysis of brain images)
Reconstruct (Boston University and Medical College of Georgia)
RView
scanSTAT (Mark Cohen)
Scion Image* (Scion Corporation)
seg (Center for Neuroscience, University of California, Davis)
ShapeLogic (Sami Badawi)
SHIVA (Laboratory of Neuro Imaging, UCLA)
siViewer (Soft Imaging System)
Skandha4 and Brain Mapper (University of Washington)
SnPM - Statistical Nonparametric Mapping (Department of Biostatistics, University of Michigan)
SPM5 (Wellcome Department of Imaging Neuroscience, 12 Queen Square, London WC1N 3AR, UK.)
SPM8 (Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology)
StackVis (Center for Neuroscience, University of California, Davis)
STASSIS (International Center for Neurological Restoration)
Statistically-based Simulation of Deformations (SBIA, Department of Radiology, University of Pennsylvania)
Stereo Investigator (Stereology System for brightfield, fluorescence and confocal microscopy)
Stimulate (CMRR - University of Minnesota)
STRFPAK (Theunissen Lab and Gallant Lab, UC-Berkeley)
stroketool (Digital Image Solutions)
stroketool-CT (Digital Image Solutions)
SuMS (Washington University School of Medicine)
SureFit (Washington University in St. Louis School of Medicine)
Surface-Based Atlases (Washington University School of Medicine)
SurfRelax (Software for surface analysis; Biomedicon/New York University)
Synu (National Center for Microscopy and Imaging Research)
Talairach Daemon (Research Imaging Institute, UTHSC San Antonio)
TetSplit (SBIA, Department of Radiology, Upenn)
TOPPCAT (Duke University Medical Center)
TurtleSeg (MIAL, Simon Fraser University and BiSICL, University of British Columbia)
Valmet (University of North Carolina at Chapel Hill, Psychiatry and computer sciences departments)
VA_SLICER (University of Minnesota)
Videoscribbler (Live video stereology overlay for Macintosh)
ViPAR (Image Analysis and Communications Lab (IACL), Johns Hopkins University )
VOLUME-ONE (VOLUME-ONE developers group)
VoxBo (Center for Functional Neuroimaging, University of Pennsylvania)
Voxtrace (National Center for Microscopy and Imaging Research)
VR-Render (IRCAD, Research Institute against Cancer of the Digestive Tract)
VTK CISG Registration Toolkit (CISG Guy´s Hospital London, King´s College London)
VVNT (Medical Imaging Solutions)
Wavelet Analysis of Image Registrattion (WAIR)
WFU_BPM (Advanced Neuroscience Imaging Research Core, Wake Forest University Baptist Medical Center )
WFU_PickAtlas (Advanced Neuroscience Imaging Research Core, Wake Forest University Baptist Medical Center)
XNAT (Washington University School of Medicine)
XnView (Gougelet Pierre)
xv* (John Bradley)
xvol (Center for Morphometric Analysis, Massachusetts General Hospital)
ZFIQ (Center for Biomedical Informatics, TMHRI-Weill Cornell)