Auswertung - (funktionelle) Magnetresonanztomographie (MRI)

AFNI und SUMA von Bob Cox am National Institute of Mental Health
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, HP, Solaris, and Linux. It is available free (in C source code format, and some precompiled binaries) for research purposes.
SUMA is a program that adds cortical surface based functional imaging analysis to the AFNI suite of programs . SUMA allows the viewing of 3D cortical surface renderings, the mapping of volumetric data onto them and, in future incarnations perform surface based computations and statistical inferences.

Analyze von Mayo Clinic
The Analyze software system is entirely built upon a toolkit of optimized functions that are organized into a software development library called AVW. Analyze offers an intuitive windows-based interface which makes it easy to learn and to use.

BIC Software Toolkit (MINC) vom McConnell Brain Imaging Center (BIC) des Montréal Neurological Insitute (MNI) an der McGill University
The BIC Software Toolkit (MINC) consists of five fundamental types of software programs. (1) Visualisation Tools: Interactive visualisation tools help you interact with imaging data directly, manipulate slices, manually segment images, superimpose different imaging modalities such as PET and MRI, etc. . (2) Basic Tools: These are non-interactive, usually run quickly and only perform some minor operations on images. (3) Advanced Image Processing Tools: These packages are non-interactive, and perform one algorithm or another on an input image in order to produce a modified output image. The four most commonly used tools here are image registration, non-uniformity correction, classification, and segmentation. (4) Pipelining Tools: These tools are designed to manipulate large data-sets, usually performing a sequence of operations on each image in the data-set. This is especially useful for clinical trials or large-scale studies. (5) Statistical Analysis Tools: These are related to performing statistical analysis on medical images, whether it be measuring atrophy or rCBF.

BRAIN von C. R. Genovese
BRAIN is a fMRI atatistical analysis software.

Brain Voyager QX und Turbo Brain Voyager (TBV) von Brain Innovation
BrainVoyager is a highly optimized and user friendly software package for the analysis and visualization of functional and structural magnetic resonance imaging data sets.
Turbo-BrainVoyager (TBV) is a highly optimized, easy to use software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. Turbo-BrainVoyager allows to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM).

CARET von Van Essen Lab an der Washington University in St. Louis
Caret includes more than 200 options for various aspects of surface visualization, manipulation and analysis. These are selected using convenient toggle buttons and pull-down/tear-off menus, with information about each option accessible via an online manual.

DTI Studio von Johns Hopkins Medical Institute

FIASCO von CMU Department of Statistics
FIASCO is a collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the output are statistical brain maps showing regions of neural activation.

FMRILAB für MatLab von Swartz Center for Computational Neuroscience
FMRLAB is a MatLab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive MatLab graphic user interface (GUI). All the necessry processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with MatLab scripts using the FMRLAB functions and data structure.

FSL von der Image Analysis Group am FMRIB
FSL (FMRIB Software Library) is a comprehensive library of functional and structural brain image analysis tools, written mainly by members of the Image Analysis Group, FMRIB, Oxford, UK. It runs under Linux, Macos X, Windows XP, SunOS and IRIX and is very easy to install. Most of the tools can be run both from the command line and as GUIs ("point-and-click" graphical user interfaces). FSL includes functional tools (FEAT, MELODIC), structural tools (BET, SUSAN, FAST, FLIRT, FUGUE, SIENA) and other tools (FSLView, AVWUTILS, MISCVIS, IRVA).

FreeSurfer mit FSFast von CorTechs und dem Martinos Center for Biomedical Imaging (MGH)
FreeSurfer is a set of semi-automated tools for reconstruction of the brain’s cortical surface and overlay of functional data onto the reconstructed surface.

LIPSIA von Dr. G. Lohmann am Department of Neurology Prof. Dr. D. Yves von Cramon
The analysis of fMRI data comprises various aspects including filtering, spatial transformation, statistical evaluation as well as segmentation and visualization. A number of well established and peer-reviewed algorithms were implemented in Lipsia that allow an efficient and user-friendly processing of fMRI data sets. The statistical evaluation in Lipsia is based on the general linear model. Various hemodynamic modelling functions are supported. In its statistical methodology, Lipsia closely follows well-established techniques. Other parts of the software such as registration, segmentation and visualization are algorithmically novel.

MEDx von Medical Numerics
MEDx is highly optimized, portable software for the visualization, processing, and analysis of medical images. Designed especially for medical imaging researchers and system developers, MEDx brings multi-modality, multi-dimensional image processing functionality to the medical imaging research community. With MEDx, users display images and control menus using the industry-standard XWindow display system and Tcl/Tk interface language. MEDx transforms your computer into a powerful image processing workstation that displays, analyzes, and processes your medical image data in a myriad of innovative ways.

MedINRIA is a free collection of softwares developed within the Asclepios research project. It aims at providing to clinicians state-of-the-art algorithms dedicated to medical image processing and visualization - in particular diffusion tensor images (DTI). Efforts have been made to simplify the user interface, while keeping high-level algorithms. MedINRIA is available for Microsoft windows XP/Vista, Linux Fedora Core, MacOSX, and is fully multithreaded.

PyMVPA von M. Hanke, Y. Halchenko, P. Sederberg und E. Olivetti
PyMVPA stands for MultiVariate Pattern Analysis (MVPA) in Python. PyMVPA is a Python module intended to ease pattern classification analyses of large datasets. In the neuroimaging contexts such analysis techniques are also known as decoding or MVPA  analysis. PyMVPA provides high-level abstraction of typical processing steps and a number of implementations of some popular algorithms. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run.

SPM für MatLab von Welcome Department of Cognitive Neurology
Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical process used to test hypotheses about [neuro]imaging data from SPECT/PET & fMRI. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT and similar modalities. Future releases will incorporate the analysis of EEG and MEG.

Stimulate von J. P. Strupp am Center for Magnetic Resonance Reseach an der University of Minnesota
Stimulate is a GUI (Graphical User Interface) based fMRI (functional Magnetic Resonance Imaging) analysis software package. It offers a comprehensive set of fMRI analysis tools integrated into a single package that was designed for both convenient and flexible data processing. The user-friendly GUI allows the user to simply "point and click" with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto aMRI (anatomic MRI) image displays.

VoxBo von Center for Functional Neuroimaging der University of Pennsylvania
VoxBo is a free software package for functional neuroimaging data analysis and presentation.

fMRI Analysis Package für MatLab von Dr. P. Skudlarski am Yale MR Imaging Research Center
The fMRI Analysis Package allows for analysis of motion and ghost artifacts and provides a wide spectrum of statistical tools to be applied to data. Processed statistical parametric maps (SPM) may be created using an array of modified t-statistics, non-parametric statistics, Fourier analysis and time-course correlations. Several pre- and post-processing filters can be applied to account for spatial correlations in images. SPM can be later viewed in many different ways and combined between different tasks and/or subjects. The intersubject comparisons are performed using the standard Talairach Tournoux atlas.

mri3dX von K. Singh an der Aston Univsersity, Birmingham
mri3dX is an integrated tool for visualization and analysis of structural and functional magnetic resonance images. It runs on most unix workstations, but requires Motif and OpenGL/Mesa graphics libraries. It is free for educational research.

nordicBrainEx und nordicICE von NordicNeuroLab
nordicBrainEx is a new BOLD fMRI and DTI analysis and visualization software for presurgical brain mapping. nordicBrainEx addresses key issues in analyzing functional MR data within the clinical workflow.
nordicICE is a general-purpose image processing and analysis software application with emphasis on the clinical use of functional imaging methods. nordicICE is a module-based solution for BOLD, Diffusion/DTI, and Perfusion/DCE imaging.

Camino von UCL Microstructure Imaging Group (MIG) am University College London (UCL)
Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.

TrackVis und Diffusion Toolkit von R. Wang und Van J. Wedeen am Athinoula A. Martinos Center for Biomedical Imaging des Massachusetts General Hospitals (MGH)
TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography.
Diffusion Toolkit is a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. Basically, it does the preparation work for TrackVis.

VISTASOFT von VISTA Lab an der Stanford University
VISTASOFT is a set of software tools that include methods for processing anatomical, functional, and diffusion tensor imaging data. The software is written mainly in Matlab. There are some additional utilities written in C++/VTK. All of the software runs on Windows/XP and on Linux (Red Hat). Most of the software runs on Apple computers. The softare tools include:
mrVista: Mister Vista is a package of the main analysis tools (includes cvs modules mrLoadRet-3.0, mrDiffusion, Anatomy, filters, mrFlatMesh and mrAlign).
mrDiffusion: This diffusion imaging analysis and visualization package requires several components from mrVista, thus this package is included in the entire VISTASOFT distribution.
ITKGray: This ITKSnap segmentation tool includes most of functionality from mrGray to this app and uses as a cross-platform replacement for the aging mrGray, which is a Windows-only app.
mrGray: This is a windows application for white-gray segmentation and 3-d viewing. mrGray is being replaced by the new project ITKGray.
vistadisp: This includes experimental control code to run under the PsychToolbox on OS-X.

Auswertung - PET/SPECT

SPM für MatLab von Welcome Department of Cognitive Neurology
Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical process used to test hypotheses about [neuro]imaging data from SPECT/PET & fMRI. These ideas have been instantiated in software that is called SPM. The SPM software package has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT and similar modalities. Future releases will incorporate the analysis of EEG and MEG.



Auswertung - Hilfsmittel zu (f)MRI, PET, ...

MR Viewer, Image Processor und Visualizer von Source Signal Imaging
MR Viewer, Image Processor, and Visualizer are part of the EMSE Suite software package for 4D multimodal functional brain imaging, including analysis, source estimation, image processing, and visualization.
MR Viewer displays magnetic resonance and other images, with specialized features designed for the overlay of electromagnetic source estimation and other functional imaging data. Seeded dipoles may be obtained (e.g. from fMRI data) for use with Source Estimator. Image data may be input in raw byte, raw word, ACR/NEMA/DICOM, and several proprietary formats. MR Viewer is the base module for Image Processor and Visualizer.
Starting with a volumetric dataset from the MR Viewer base module, Image Processor tools support segmentation, boundary mesh generation, and cortical unfolding. The output may be made available to Visualizer for 3D rendering, or to Source Estimator for realistic headshape modeling and cortical surface restriction.
Use Visualizer to obtain and view 3D rendered images, combining data from several modalities, including topographic mapping, MRI data and electromagnetic source analysis.

Talairach Daemon von Research Imaging Center der University of Texas
The Talairach Daemon (TD) is a high-speed database server for querying and retrieving data about human brain structure over the internet. The TD server data is searched using x-y-z coordinates resolved to 1 x 1 x 1 mm volume elements within a standardized stereotaxic space. Coordinates tracked by the TD server are spatially consistent with the Stereotaxic Atlas of the Human Brain (Talairach and Tournoux, 1988).

MRIcro von C. Rorden an der University of Nottingham
MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms.

iiV von der Cognitive Neuroimaging Unit an der University of Minnesota
iiV (formerly CNUViewer) is a brain imaging data display tool written in Java1.1.

mni2tal und tal2mni für MatLab von der MRC Cognition and Brain Sciences Unit
These MatLab programs transform MRI (based on standard brains from the Montreal Neurological Institute) brain coordinates to Thalairach (used in Talairach and Tournoux atlas) brain coordinates and vice versa.

mrGray und mrFlatMesh von Dr. Wandell an der Stanford University
The segmentation and flattening tools distributed at this site permit you to identify the gray matter in visual cortex and then to produce a visualization of the gray matter in a single plane.

WFU_PickAtlas vom Advanced Neuroscience Research Core an der Wake Forest University
The PickAtlas software toolbox provides a method for generating ROI masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy) and Tissue Type. The atlases have been extended to the vertex in MNI space (see Atlas Modifications under Technical Notes). Additional atlases (including non-human atlases) can be added without much difficulty. The wfu_pickatlas tool requires at least Matlab 6.0, and is compatible with SPM99, SPM2 and SPM5. The toolbox has been evaluated on Sun Solaris and Linux platforms. It has not been extensively evaluated for Windows.

SurfStat von K. J. Worsley am Department of Mathematics and Statistics an der McGill University
SurfStat is a Matlab toolbox for the statistical analysis of univariate and multivariate surface and volumetric data using linear mixed effects models and random field theory. It is inspired by Jason Lerch's Thickness Statistics written in R, and Jonathan Taylor's BrainStat, part of NIPY, written in Python. It is intended for cortical thickness data on triangular meshes, either for the whole cortex or one for each hemisphere. It will handle any triangulated surface data, written in FreeSurfer or MNI object format.

REST von State Key Laboratory of Cognitive Neuroscience and Learning an der Beijing Normal University
Resting-State fMRI Data Analysis Toolkit (REST) is a 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. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract ROI time courses, reslice images, and sort DICOM files.

LIBSVM von C.-C. Chang und C.-J. Lin vom Department of Computer & Information Engineering an der National Taiwan University
LIBSVM is a library for support vector machines.

BrainVISA / Anatomist
BrainVISA is a software, which embodies an image processing factory. A simple control panel allows the user to trigger some sequences of treatments on series of images. These treatments are performed by calls to command lines provided by different laboratories. These command lines, hence, are the building blocks on which are built the assembly lines of the factory.
Anatomist is a visualization software, which main originality is a generic module dedicated to structural data, namely sets of objects linked one another into a graph structure. These objects may be cortical folds inferred from T1 weighted MR data, fiber bundles inferred from MR diffusion weighted data, activated clusters inferred from Statistical Parametric Maps, etc... This module includes a nomenclature control panel, which can drive several brains simultaneously. Anatomist provides also some tools to easily map Statistical Parametric Maps on 3D renderings of the brain, inflated meshes of the cortical surface, etc... Finally, a manual drawing toolbox can be used for various purpose.

Dipy is an international, free and open soure software project for diffusion magnetic resonance imaging analysis. Depends on a few standard libraries: python (the core language), numpy (for numerical computation), scipy (for more specific mathematical operations), cython (for extra speed) and nibabel (for file formats). Optionally, it can use python-vtk (for visualisation), pytables (for handling large datasets), matplotlib (for scientific plotting), and ipython (for interaction with the code and its results). Dipy is multiplatform and will run under any standard operating systems such as Windows, Linux, Mac OS X.

Fibernavigator ursprünglich vom Institut für Informatik der Universität Leipzig
Fibernavigator is a tool for visualization of dti and mri data. This project is dedicated to the development of fast and versatile visualization of results of deterministic tractography, including effective selection of fibres, to the effective visualization of probabilistic tractograms, including surface texturing, and to the integration of fibre visualization with the display of MRI, functional MRI and EEG/MEG source localization results

Huettel, S. A., Song, A. W. & McGarthy, G. (2008). Functional magnetic resonance imaging (2nd ed.). Sunderland, MA: Sinauer Associates.
Talairach, J. & Tournoux, P. (1988). Co-planar stereotaxic atlas of the human brain. 3-dimensional proportional system: An approach to cerebral imaging. Suttgart: Thieme Verlag.

Weitere Überblicksseiten:
Brain Software von THOR Center for Neuroinformatics

Free Medical Imaging Software von I do Imaging


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