Tool/Resource Listing

DFBIdb

DFBIdb is a suite of tools for efficient management of neuroimaging
project data. Specifically, DFBIdb was designed to allow users to quickly
perform routine management tasks of sorting, archiving, exploring, exporting
and organising raw data. DFBIdb was implemented as a collection of Python
scripts that maintain a project-based, centralised database that is based on the
XCEDE 2 data model. Project data is imported from a filesystem hierarchy of
raw files, which is an often-used convention of imaging devices, using a single
script that catalogues meta-data into a modified XCEDE 2 data model. During
the import process data are reversibly anonymised, archived and compressed.
The import script was designed to support multiple file formats and features an
extensible framework that can be adapted to novel file formats. Graphical user interfaces are provided for data exploration. DFBIdb includes facilities to export, convert and organise customisable subsets of project data according to user-specified criteria.

dtiBrainScope

This is a software package for processing diffusion tensor imaging data. The following functions are included:
1. Converting imaging data in DICOME format to ANALYZE format
2. Extracting binary brain mask for quick scalp-removing
3. Correcting eddy-current induced distortion
4. Optimized tensor estimation based on noisy diffusion-weighted imaging (DWI) data
5. Scalp removal using a brain mask image
6. Corregistering imaging data and generating deformation field for mapping images from individual spaces to a template or target space
7. Spatial Normalization and Warping DTI
8. Fiber tracking
9. Clustering fiber tracts
10. Identifying brain ventricles and generating binary masks for the baseline and DW imaging data
11. Deriving diffusion anisotropy indices (DAIs) and principal directions (PD) and the corresponding color-coded PD-map.

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). It has been used for fMRI analysis, e.g.

CLEAVE adds the following to the standard ANOVA analyses:

0) Unlimited numbers of factors can be analyzed.
1) Factor Correlation and Unequal Variance Corrections
2) Treatment Magnitudes: omega^2, partial eta^2, and R^2
3) A convenient Ranking of Factors based upon treatment magnitudes and significance levels.
4) Post-Hoc Significance Tests
5) Post-Hoc Power Table to gauge how many subjects will be needed to achieve significance.
6) Allows the use of Random Factors.
7) A Configuration File to make the program more tunable
8) A Histogram and Cell Line Diagrams: which help the user to detect outliers.
9) Associated MATLAB functions: read CLEAVE-style data sets into MATLAB and write data back out in a CLEAVE-ready format.

Software is at http://www.ebire.org/hcnlab/software/cleave.html

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.
Various tract-oriented scalar diffusion measures obtained from DTI brain images, are treated as a continuous function of white matter fibers' arc-length. To analyze the trend along a given fiber tract, a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows (along the tract), such that they best represent the data and are robust to noise and Partial Volume effect.

The features available in the tool currently, its use and input / output formats and other relevant details are provided in the first draft of the documentation. (http://www.na-mic.org/Wiki/index.php/Projects:dtistatisticsfibers).

GesTr

GesTr is a cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons.

GesTr supports simple XML files to customize recognized gestures and their corresponding actions.

GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device.

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. 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.

Most recent version and any questions could also be checked out in: http://www.restfmri.net .

Temporal-lobe.com

Existing knowledge of hippocampal - parahippocampal connections was integrated into an interactive diagram in which any connection can be turned on or off at the level of cortical layers.

Project Goals:
* To provide an overview of all known anatomical projections of the rat hippocampal - parahippocampal network.
* To provide a graphical interface with which users can turn on or off any connections at regional level down to the level of cortical layers.
* To make it easy to find references for a particular projection.

Download the diagram for free at www.temporal-lobe.com.

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. Our current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, we hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships.

Please visit our website (nidag.org) and sign up to join our mailing list. We are interested in hearing from people who might be willing to contribute to our projects, particularly those with programming experience.

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. 51, No. 3, 1 July 2010, pp. 1057-1070.

The package is available free to the public for the academic research purpose at http://bric.unc.edu/ideagroup/free-softwares/.

The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5).

This software was developed in IDEA group in UNC-Chapel Hill. For more information, please visit our lab at http://bric.unc.edu/ideagroup.

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. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers.

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. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.

Mesh-based Monte Carlo (MMC)

Mesh-based Monte Carlo, or MMC, is a Monte Carlo (MC) solver for photon migration in 3D turbid media. Different from existing MC software designed for layered (such as MCML) or voxel-based media (such as MMC or tMCimg), MMC can represent a complex domain using a tetrahedral mesh. This not only greatly improves the accuracy of the solutions when modeling objects with smooth/complex boundaries, but also gives an efficient way to sample the problem domain to use less memory. The current version of MMC support multi-threaded programming and can give a almost proportional speed-up when using multiple CPU cores.

Monte Carlo eXtreme (MCX)

Monte Carlo eXtreme, or MCX, is a Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470.

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. It contains a rich set of mesh processing scripts/programs, functioning independently or interfacing with external free meshing utilities. Iso2mesh toolbox can operate directly on 3D binary, segmented or gray-scale images, such as those from MRI or CT scans, making it particularly suitable for multi-modality medical imaging data analysis or multi-physics modeling.

URL: http://iso2mesh.sf.net

Template Image Processing Library

Template Image Processing Library (TIPL) is a lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an "easy-to-use" and also "ready-to-use" library.

The code is template-based, and only header files are needed to be included to the source code.

This library provides the following functions:
1.DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w)
2.numerical: add, multiply, gradient.
3.interpolation: linear, gaussian radial basis
3.filters: mean, gaussian, laplacian, sobel, anisotropic diffusion
4.morphological processing: erosion, expansion, opening, closing
5.template-based Fourier transform
6.linear coregistration: rigid body, affine transform, least square fit, mutual information
7.nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM)

Automatic Segmentation Tool Adapter

More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency.

In this project, we will provide an open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community.

Vervet Probabilistic Atlas

The vervet (Chlorocebus pygerythrus) probabilistic atlas defines an anatomical space (template) with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The "Biased" directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The "Unbiased" directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas, for example those in Slicer.

Spanish Resting State Network

Spanish Resting State Network (SRSN); Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de España y centros nacionales e internacionales.

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. It is a matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions.

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.

The Neuro Bureau

The Neuro Bureau is neuro-collaboration in action.

More specifically, Neuro Bureaus around the world offer the opportunity for common working spaces devoted to neuro-related interests.

If you would like to found a Neuro Bureau in your own city, or for more information, please contact:
info(at)neurobureau.org

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. The registration toolbox has 2 options: 1) a Mutual Information based registration, 2) a Sum-of-Square differences registration method. The final output is in the same space as the fixed image. You do require to have CUDA v2.2 or greater installed on your system with atleast 256MB Nvidia GPU memmory card. All operating systems are supported, but take a look at the CMakeLists.txt file for how to compile for you system.

V3D and V3D-Neuron

V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. In short, V3D streamlines the workflow of visualization-assisted analysis.

V3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to V3D Plugins.

V3D-Neuron is built upon V3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, Vol. 28, No. 4, pp. 348-353, DOI: 10.1038/nbt.1612.) about V3D and V3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.

The fMRI Data Center

A free database of fMRI data used in peer reviewed studies. The database of studies can be browsed and searched, and data is provided via download links that are emailed to users in response to specific requests. All of the data has been rendered anonymous, is free, and can be used in further studies. Any published findings based on these datasets should credit the authors of the original study as well as the fMRI Data Center including the accession number.

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.

NIPY Diffusion Imaging Analysis

DiPy is a python package for analyzing diffusion data.

NIPY File IO

NiBabel is a Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.

NIPY Timeseries Analysis

Nitime is a library for time-series analysis of data from neuroscience experiments.

It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

MATLAB Tutorial on Diffusion Tensor MRI

This is an on-line tutorial on how to use MATLAB for Diffusion-Weighted MRI processing. The following subjects are covered in this tutorial: Generation of Synthetic Diffusion-Weighted MRI datasets, Diffusion Tensor (DTI) Estimation from DW-MRI, DTI Visualization as a field of ellipsoids, Higher-order Diffusion Tensor Estimation from DW-MRI, Computing of Tensor Orientation Distribution Functions (Tensor ODF), Computing of Fiber Orientations, Higher-order Diffusion Tensor Image Visualization as fields of spherical functions, Multi-fiber reconstruction etc.

The tutorial contains numerous illustrations, figures and Matlab scripts embedded in the text. The reader/user can automatically generate Matlab script for a self-designed DW-MRI experiment by selecting which steps needs to be followed. The code that corresponds to the selected steps is then appropriately merged in the "Matlab Script Generator", and the user can easily copy and paste the produced code directly to the Matlab command prompt.

PyNIfTI

The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.

NIPY Community

The purpose of NIPY is to make it easier to do better brain imaging research. We believe that neuroscience ideas and analysis ideas develop together. Good ideas come from understanding; understanding comes from clarity, and clarity must come from well-designed teaching materials and well-designed software. The software must be designed as a natural extension of the underlying ideas.

We aim to build software that is:

* clearly written
* clearly explained
* a good fit for the underlying ideas
* a natural home for collaboration

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://tinyurl.com/2e5zwen)

PsychoPy

PsychoPy - Psychology software in Python. PsychoPy is an open-source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.

NIPY Structural and Functional Analysis

Nipy aims to provide a complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

GAMMA

GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis.

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. Neophytes to the Pipeline can have their own private server running in minutes, software engineers and workflow designers can use the PNVE as a sandbox, and those without access to grid computing facilities can now take full advantage of the Pipeline processing environment.

NeuroDebian

This is a collaborative effort to package neuroscience-related software for the Debian operating system. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well.

With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. For example, installing FSL looks like: "apt-get install fsl"

There is also virtual machine to test NeuroDebian on Windows or Mac OS.

If you want to see your software packaged for Debian, please drop us a note.

SFMProject

Structure from motion algorithms repository. Common interface for various sfm algorithms.

Whole Brain Catalog

A 3d atlas of the mouse brain that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework.

Parkinson's Disease Discovery Database

Tools will be available for biomedical data mining and visualization as well as linkages to Google Maps and other online resources.

PESTICA fMRI Physio Detection/Correction

Do you have 3D+time EPI data (BOLD or perfusion) but no usable physio signals for pulse and respiration? Are you concerned about the effect of physio noise on your data but don't know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal? This is for you. This distribution includes a tool (Physiologic EStimation by Temporal ICA or PESTICA) to detect physiologic signals _from the data itself_! These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal.
Are you concerned about the number of regressors you're incorporating once you add 5th order RETROICOR (20 more regressors!)? The other half of PESTICA is an adaptive physiologic noise removal tool (Impulse Response Function or IRF-RETROICOR) that zooms in on noise with only 6 regressors, getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have.

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. See http://www.miccai2010.org/

This project will support community outreach and dialog between presenters and audience, both before and after the tutorial session, and is intended to engage the broader community in the deliberations on this important topic.

"Best Practices" will cover software engineering practices as well end-user installation and support practices.

BioMesh3D

BioMesh3D is a free, easy to use program for generating quality meshes for use in biological simulations. It is included when downloading SCIRun v4.4.

SCIRun

SCIRun is a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.4.

ImageVis3D

ImageVis3D is a new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with our collaborators.

iBrain™ Laterality Toolbox

The iBrain Laterality Toolbox contains Matlab scripts that implement an objective threshold-independent assessment of whether the balance of activity between two regions of interest is typical or atypical, based on statistical comparison between an individual and a group of controls. The toolbox displays laterality index (LI) plots as a function of an adaptive threshold, and provides statistical assessment of the plots to determine lateralisation. The method is described in the following paper:

Abbott DF, Waites AB, Lillywhite LM, Jackson GD.
fMRI assessment of language lateralization: An objective approach.
Neuroimage 50(4):1446-1455 (2010).

This toolbox is compatible with SPM2, SPM5 and SPM8.

The data on which the toolbox operates need not have been generated by SPM.

ConnectomeViewer

ConnectomeViewer is free, open source, cross-platform Python-based software application for visualization and analysis in connectome research.

Features of the software include:
* Connectome File Format including metadata, networks, surfaces, volumes, track files
* Complex network analysis toolboxes
* Modular plugin architecture for extensibility
* Mayavi2 for 3D Scientific Visualization and Plotting
* Interactive data manipulation and scripting capabilities
* Neuroimaging and Diffusion in Python libraries

ConnectomeWiki Knowledge Base

ConnectomeWiki is a knowledge base for macro- and mesoscale brain region and brain connectivity information across species. It is built using modern semantic wiki technology, meaning that it is a resource added to and maintained by a community of users.

Sophisticated semantic search queries, references to relevant papers about regions and connectivity, links to other databases, different brain partition schemes and their relation are some of its features.

eConnectome

eConnectome (Electrophysiological Connectome) is an open-source MATLAB toolbox for imaging brain functional connectivity from electrophysiologic signals (http://econnectome.umn.edu/). It provides interactive graphical interfaces for EEG/ECoG preprocessing, source estimation, connectivity analysis and visualization. The current release allows connectivity imaging from EEG and ECoG over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB.

eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome "La Sapienza".

Generalized Covariance Analysis (gCVA)

Generalized Covariance Analysis: a platform for any PCA-based analysis on functional neuroimaging data (PET and fMRI).

Includes:

- Ordinal Trend Canonical Variance Analysis for parametric designs
(C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645)

- Partial Least Squares for any design matrix

- Subprofile Scaling Model for cross-sectional designs
(JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.)

NIPY Pipeline and Interfaces

Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow.

Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

SCRalyze

SCRalyze is a powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.

Non-rigid groupwise registration method

The goal of the project is to provide an open source implementation of a non-rigid groupwise registration method.

This project is implemented by
+ Serdar K Balci (serdar at csail.mit.edu)
and supervised by
+ Polina Golland
+ William M. Wells

All metrics are implementing in a multi-threaded fashion. The algorithm will run faster on
computers with multiple CPU's.

Fluid Registration and Atlas Toolkit

FRAT provides c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are:

LDDM: Fluid registration between two images.
TimeSeries: Time series analysis of longitudinal data for a single subject.
AtlasBuilder: Cross-sectional atlas building for a population of images.
LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set.
FRATUtils: A collection of utility functions for working with volumes and time series files

CAMINO-TRACKVIS

With increasing efforts on brain connectivity analyses it becomes important to have tools that can allow increased interoperability among different tractography tools. This package allows interoperability between CAMINO and TRACKVIS. CAMINO is a leading software package in DTI processing. The package is from University of College London. TRACKVIS is a tract visualizing utility with capability of visualizing up to and over a million white matter tracts seamlessly. The package is from Massachusetts General Hospital.

The tools in this package allow conversion of tracts from one format to another in a very effective way with ability to handle over a million tracts.

Pipeline system for Octave and Matlab

A pipeline is a collection of jobs, i.e. matlab or octave codes with a well identified set of options that are using files as inputs and are producing files as outputs. PSOM is a framework to implement, run and re-run pipelines in Matlab or Octave :

* Describe the pipeline using a straightforward structure representation.
* Automatically generate log files and keep track of the pipeline description.
* Handle job failures : successful completion of jobs is checked and failed jobs can be restarted.
* Handle updates of the pipeline : change options or add jobs and let PSOM figure out what to reprocess !
* Automatically run jobs in parallel whenever possible using multiple CPUs or within a distributed computing environment.

DIAMOND

UC Davis IDeA Lab Applications for Management Of Neuroimaging Data -
View dicom files and assemble them into 3D volumes.
View and convert between Analyze, Nifti, and Interfile.
Classify and organize dicoms and 3D volumes using metadata.
Search and report on a collection of scans.

Multi-Modal MRI Reproducibility Resource

We have acquired scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease). Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format and will be publicly released at the earliest opportunity.

This is intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic "1 hour" session at 3T.

Please cite: Bennett A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study. Submitted 2010

DTIProcess ToolKit

DTIPrpcess is a DTI processing and analysis toolkit developed in UNC and University of Utah. Tools in this toolkit include dtiestim, dtiprocess, dtiaverage, fibertrack, fiberprocess, et al..

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).

JIP fMRI Analysis Toolkit

The JIP Toolkit was developed primarily for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for time series analysis (2nd-order GLM analysis following the Worsley 2002 scheme is coming soon), 4) MRI templates to place your rodent and non-human primate data into standardized spaces.

BrainVoyager QX

BrainVoyager QX is a powerful neuroimaging software package. It started as a tool for the analysis of anatomical and functional MRI data sets but has evolved over the years into a multi-modal analysis tool for fMRI, DTI, TMS, EEG and MEG data. The software is highly optimized and user friendly running on all major computer platforms including Windows (XP/Vista/7), Linux (i.e. Ubuntu, SUSE, Fedora) and Mac OS X (10.4 or higher including Snow Leopard).

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. SPHARM-PDM is a tool that computes point-based models using a parametric boundary description for the computing of Shape analysis.

The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speciﬁc locations.

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.

Includes:
* High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor
* Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room
* 30 meter fiber optic cable that runs between the projector and projector control station
* Heavy duty, magnet compatible, projector stand (assembly required)
* Heavy duty, magnet compatible mirror stand with mirror (assembly required)
* High resolution, lenticular pitch rear projection screen for high quality image reproduction
* Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended)

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. Since it is written in Java, it can run on a wide variety of computers.

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.

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.

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. SHIVA can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets.

MultiTracer

MultiTracer (http://www.loni.ucla.edu/Software/MultiTracer) is a Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision.

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. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs.

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. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

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. It simplifies the creation of application programs by providing a ready-made set of support routines.

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).

* Infrastructure Resources (Databases, computational Grid, services).

* Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data).

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. The processing pipeline includes image registration, filtering, and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program.

1000 Functional Connectomes Project

On behalf of the ‘1000 Functional Connectomes’ Project, we are pleased to announce the unrestricted public release of 1200+ ‘resting state’ functional MRI (R-fMRI) datasets independently collected at 33 sites. All datasets have been generously donated by the principal investigators from the member sites, for the purpose of providing the broader imaging community complete access to a large-scale functional imaging dataset. Age, sex and imaging center information are provided for each of the datasets. In accordance with HIPAA guidelines, all datasets are anonymous, with no protected health information included. We anticipate this data-sharing effort will equip researchers with a means of exploring and refining R-fMRI approaches, and facilitate the growing ethos of sharing and collaboration.

Disclaimer: The '1000 Functional Connectomes Project' datasets are provided freely without assurance of quality or appropriateness for usage.

**SELECT 'SEE ALL FILES' FOR DOWNLOAD LIST (NOT DOWNLOAD NOW)**

BrainSolution

BrainSolution is a collection of tools for MRI T1 brain image segmentation in the Windows® environment. It helps construct a complete pipeline with necessary preprocessing and postprocessing procedures besides brainparser, the core program of our fast brain segmentation. The execution of the whole pipeline can be completed in 2 hours with good segmentation results.

shapeAnalysisMANCOVA - SPHARM tools

shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues.

Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124

MRI_CVPR

Tools processing MRI data with a number of techniques from cvpr conference, including segmentation, matching, features, and classification.

ValMap: simple statistical mapping tool

valmap is a command line voxel-wise statistical analysis program for images. Images can be gray matter density, jacobian images, etc.

The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix.

Why use valmap?

1. Do not need a Matlab license to run.
2. Can incorporate a spatially varying independent variable (e.g., you have a perfusion map as your dependent variable, and you want to co-vary for gray matter at each voxel, so use a gray matter map as an independent variable).
3. Can use spatially invariant independent variables (e.g., you can have a cognitive test score as the dependent variable, and use jacobian maps as the independent variable).
4. Can have multiple dependent variables and do multivariate analyses (e.g., want to know the overall effect of disease on perfusion and structure, so use perfusion maps and jacobian maps as dependent variables).

Analyze

Analyze provides an integrated, comprehensive set of tools for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data. With Analyze, both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships.

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. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper "Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis" (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage.

TORTOISE

The TORTOISE software package is for processing diffusion MRI data. It contains two main modules, DIFF_PREP and DIFF_CALC.

DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space

DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis

Software and sample data downloads, as well as documentation for the software, are available at http://www.tortoisedti.org.

UNC Human Brain Atlas

3 human brain atlases have been created at UNC-Chapel Hill: a pediatric, an adult and an elderly one. They include overall a T1-weighted image (with and without skull), subcortical structures probability maps, tissue segmentation probability maps and a parcellation map.

Waxholm Space Atlas

Here you can download image volumes representing the canonical Waxholm Space (WHS) mouse brain. These images include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel), and a label volume describing 37 structures. All volumes are represented at 21.5μ isotropic resolution.

DWI/DTI Quality Control Tool: DTIPrep

DTIPrep performs a "Study-specific Protocol" based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing.

Brainstorm

Brainstorm is a free Matlab application dedicated to MEG and EEG data visualization, processing and cortical source estimation.
Its rich and intuitive graphic interface does not require any programming knowledge or experience with Matlab.

MEG/EEG visualization and processing:
- Support for most of the common file formats for MEG, EEG and MRI
- Basic pre-processing: frequency filtering, resampling, epoching, baseline removal, averaging, etc.
- Visualization of recordings: time series, 2D/3D topographies
- MRI/EEG/MEG co-registration
- Database and powerful database explorer

Source estimation:
- Forward modeling: spherical models, overlapping spheres, BEM
- Inverse modeling: minimum norm, beamformers
- Visualization of sources: cortex surface, MRI volume

Post-processing:
- Definition of clusters of electrodes
- Regions of interests at cortical level
- Group analysis, registration of individual brains on a template
- Statistical tests: t-test, permutations

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.

The main focuses of this resource are the "MediaWiki" and "Forums" (in the tool bar on the left).

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.

This NITRC project site is dedicated to linking all listed connectivity analysis tools under one common heading, including HCP-related as well as independently created software. Please use this site to explore the variety of connectomics software tools available via NITRC as well well as valuable data resources, forth coming scientific meetings, etc. Scroll down to the list of associations to the current list of tools. If you have such tools yourself, please list them with NITRC, and request to link with us!

See http://www.humanconnectomeproject.org for additional details on the HCP.

The link back to this NITRC project site is http://www.nitrc.org/projects/hcp/

CONN - fMRI functional connectivity

Performs functional connectivity analyses of fMRI data.

Features: Seed-to-voxel and ROI-to-ROI analyses. Resting state and task-related connectivity analyses. Gui and batch processing.

Methods: Spatial preprocessing; CompCor method for removing physiological and other confounds; First-level univariate and multivariate regression and bivariate and semipartial correlation connectivity measures; Second level random effect analyses.

Dependencies: Matlab, SPM

http://web.mit.edu/swg/software.htm

BrainSuite

BrainSuite is a suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools.

Fiber Optic Button Response System

The Fiber Optic Button Response System accurately gathers participant responses and verifies signals. The Celeritas Series response units are assembled using high-impact, chemical resistant, medical grade plastic. The response units include a tactile indicator to ensure correct finger placement during experiments and comfortably attach to the participant’s wrists. The units communicate button presses through fiber optic cabling which connects to a Fiber Optic Interface Console located in the control room through an available wave guide. The interface console provides real-time feedback of participant responses via LED indicators and includes a set of switches which can be used to make responses for the participant as needed.

Subject Library

UC Davis IDeA Lab Applications for Management Of Neuroimaging Data --

A collection of tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks.

HD Neuro-Informatics

Huntington Disease Nueroimaging Initiative (HDNI) is an international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in HD. The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies.

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.

The resting-state fMRI images were collected on several occasions:
1. the first resting-state scan in a scan session
2. 5-11 months after the first resting-state scan
3. about 30 (< 45) minutes after 2.

Each scan occasion is released as a new version release of the resource. Make sure to check all releases to get all files.

Data use is unrestricted, but users should reference our original publications and NITRC (see Documentations).

***Caution: Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets.

Acquisition was funded by Stavros S. Niarchos Foundation, the Leon Lowenstein Foundation, NARSAD (The Mental Health Research Association) grants to F.Xavier Castellanos; and Linda and Richard Schaps, Jill and Bob Smith, and the Taubman Foundation gifts to F.Xavier Castellanos.

ASL data processing tool box

This tool box is for arterial spin labeled perfusion MRI data processing. It is based on SPM (copyright by Wellcome Department, London) and Matlab (MathWorks Inc). A more detailed documentation could be found in asl_perf_subtract.m, the main function for calculating CBF value. The current version support 3D or 4D Analyze or Nifiti format and support PASL, CASL, and PCASL data. It currently contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis. I will include some toolkits for data quality checking and data visualization. Sample data will be also provided in my webpage: http://cfn.upenn.edu/~zewang.

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. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available on NITRC). They are therefore cross-platform and compatible with a wide variety of file formats.

QCQP

Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction.

NeuroLex

The NeuroLex is being constructed to help improve the way that neuroscientists communicate about their data, so that information systems like the NIF can find data more easily and provide more powerful means of integrating data that occur across distributed resources.

One of the big roadblocks to data integration in neuroscience is the inconsistent use of terminology in databases and other resources like the literature. When we use the same terms to mean different things, we cannot easily ask questions that span across multiple resources. For example, if three databases have information about what genes are expressed in cortex, but they all use different definitions of cerebral cortex, then we cannot compare them easily.

FastICA

General-purpose unsupervised data-analysis tool, most often used for brain imaging data.

signalml

Example implementation of SignaML metadescription of formats of biomedical time series, allowing to read data in new formats base upon standardized XML description.
Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.

Mean Machine

This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz.

LONI Viz

LONI_Viz is a versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS/DXF surfaces, and atlas hierarchical brain-region labelings (Hyperbolic BrainGraph Model Display).

LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest.

Allen Brain Atlas API

API and demo application for the ABA Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast.

Free-D

Free-D allows the reconstruction of 3D models from image stacks (segmentation, registration, surface reconstruction, 3D rendering).
It is designed in the goal of non-linear spatial normalization and averaging of collections of individual 3D models (this module is currently in alpha version only and not included in the distributed version).

EEGLAB

EEGLAB provides an interactive graphic user interface allowing users to flexibly and interactively process their high-density EEG and other dynamic brain data using independent component analysis (ICA) and/or time/frequency analysis (TFA), as well as standard averaging methods.

Atlas3D

Experimental data can be imported in Atlas3D and warped to atlas space, using linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

OASIS

The Open Access Series of Imaging Studies (OASIS) is a project aimed at making MRI data sets of the brain freely available to the scientific community. By compiling and freely distributing MRI data sets, we hope to facilitate future discoveries in basic and clinical neuroscience. OASIS is made available by the Washington University Alzheimer’s Disease Research Center, Dr. Randy Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard University, the Neuroinformatics Research Group (NRG) at Washington University School of Medicine, and the Biomedical Informatics Research Network (BIRN). OASIS currently includes two data sets. A cross-sectional set includes 416 subjects aged 18 to 96, 100 of whom were clinically diagnosed with Alzheimer's disease. A longitudinal release includes 150 subjects aged 60 to 96, many diagnosed with Alzheimer's disease at some point during their participation.

factory_t1_dti

Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images.

ImageJ

(From http://rsbweb.nih.gov/ij/docs/intro.html) ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.

It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

BrainImageJava

BrainImageJava is a multiplatform, highly modular image processing and visualization application which is under development by the Center for Interdisciplinary Brain Sciences Research. The goal of this project is provide a framework application for neuroimaging which facilitates the interchange of software tools developed by researchers.

BrainImageJava can:
o Delineate ROIs in slices along X, Y, or Z axes, with 3D feedback in the other axes.
o Create and display triangular mesh surfaces from MRI volumes.
o Draw Surfaces-of-Interest (SOIs) in 3D, and edit them in a planar display.
o Set Talairach grid on a volume, export an AC/PC stack, and measure the values within each grid unit.

BRAINSROIAuto

Automatically creates a mask based on the 'foreground' of an anatomical scan volume.

Camino

Camino is a free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.

NICE-SIGN

NICE-SIGN is a nice sign of bias field correction (nonuniformity) in medical images. This tool is fast and efficient. Technical details can be found at http://zheng.vision.googlepages.com/biasCorrection_miccai09_Zheng.pdf

VR Worlds 2

VR Worlds 2 is designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs.

Create complex environments with meaningful content using VR Worlds 2’s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale.

VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including:

* Residential/Urban Area
* Hotel Lobby
* Medical Office
* Grocery Store

Quantitative Diffusion Tools

The Quantitative Diffusion Tools provide Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc.

MRI Defacer

Tool to remove facial features from an MRI structural image for the purpose of de-identification.

NC-IGT Fast Imaging Library

This software provides algorithms for the reconstruction of raw MR data. In
particular, it supports the reconstruction of accelerated data acquisitions
where k-space is subsampled and the Fourier domain encoding is complemented
by temporal encoding, spatial encoding, or and/or a constrained
reconstruction. This library of functions provides a number of
reconstruction algorithms that accurately employ advanced MR imaging methods
including: UNFOLD; parallel imaging methods such as SENSE and GRAPPA;
Homodyne processing of partial-Fourier data, and gradient field
inhomogeneity correction.

The target audience is research groups who may be interested in exploring or
employing advanced MR reconstruction techniques, but don't have the
necessary expertise in-house.

Inquires may be directed to: ncigt-imaging-toolkit -at- bwh.harvard.edu

Cytoseg

The goal of the Cytoseg project is to produce tools for automatic segmentation of of 3D electron microscopy, specifically neuropil. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools).

E-Prime Extensions for fMRI

E-Prime® Extensions for fMRI (EEfMRI) software is designed to optimize E-Prime® experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime® experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime®.

SpineSegmentation module for 3DSlicer

3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.

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.

The software includes algorithms for simple and advanced analysis of MEG and EEG data, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing. It supports the data formats of all major MEG systems (CTF, Neuromag, BTi) and of the most popular EEG systems, and new formats can be added easily. FieldTrip contains high-level functions that you can use to construct your own analysis protocols in Matlab. Furthermore, it easily allows developers to incorporate low-level algorithms for new EEG/MEG analysis methods.

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. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function. The goal of the proposed work is to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. The proposed research investigates extension of established practices for volumetric labeling and web- based collaboration to create an innovative infrastructure for labeling.

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. The toolbox is available online at http://www.brain-connectivity-toolbox.net, and runs in Matlab. Network measures include those based on degree, clustering, distance, centrality, modularity and motif count. Most measures have weighted and directed variants. In addition, the toolbox contains multiple cortical connectivity datasets acquired using tract tracing and diffusion MRI techniques. There is also a selection of methods for the generation of reference random and ordered networks.

iView X MRI-LR - Eye Tracking for fMRI

The iView X MRI-LR is a non-invasive, long-range eye tracking system for use in the fMRI environment. Some features of the system include:

- Elaborate faraday shielding and fiber optics to avoid noise in high-field magnets.

- Includes stimulus presentation software “Experiment Center” and is compatible with 3rd party products such as “Presentation” by NeuroBS.

- Utilizes mirror box customized for large field of view.

- Includes powerful analysis software “BeGaze2” for graphical and statistical analysis of eye movements.

- Includes fixation, saccade and blink detection, and area-of-interest based statistics

- Real-time data available via digital or analog output

Biomag Discussion Group on Yahoo

A discussion group for those actively involved in research into, or applications of, biomagnetism and magnetoencephalography (MEG). Continuing in the tradition of the first biomagnet host, based in Gothenburg, Sweden, which was followed by a host maintained by CTF Systems Inc. in Coquitlam BC, Canada, this is an electronic forum for discussion of topics in biomagnetism and for maintaining a database for archival and dissemination of shared information.

To get to the discussion group page click on menu item at left or copy the following to your browser address field:
http://tech.groups.yahoo.com/group/biomag/

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. FOPA is an attempt to design and implement a common protocol for network and command line communication with either file-system or imbedded data structures. Initial reference implementations will support interoperability between ITK, VTK, and Java platforms. Contributions are welcome from other neuroimaging development communities.

This project is an open community effort under the BSD license.

Presentation

Presentation® is a precise and powerful stimulus delivery and experimental control program for neuroscience. Presentation® runs on any Windows PC, and delivers auditory, visual and multimodal stimuli with sub-millisecond temporal precision. Presentation® includes special features for experiments using psychophysics, eye movements, fMRI, ERP, MEG, single neuron recording, and more.

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. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D.
Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions.

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. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.

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. It projects stereotaxic coordinates to a mean cortical surface by using an anatomical database of 60 young adults to provide multiple mappings of normalized cortical surfaces into MNI space. VAMCA performs the following analyses:

1) Multi-Fiducial Projection Mapping: Map stereotaxic 3D coordinates to the normalized cortical location for each of 60 database subjects.
2) Computing Centroid Locations for groups of foci both on a mean cortical surface and in MNI space.
3) Comparing Two Groups of Foci for differences in location (surface or 3D) of their group centroids and computing the groups' overlap extent using permutation tests.
4) Detecting Significant Densities of Foci or Density Differences of Two Groups within anatomical ROIs on a mean cortical surface by using Monte Carlo analyses. Coordinate weights allow fixed or random effects type analyses.

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.

Many more computational tools will be shared with users and developers as they become available.

Download info: http://sites.google.com/site/hispeedpackets/

ArtRepair for robust fMRI

ArtRepair is a toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change.

Multi-fiber Reconstruction from DW-MRI

This program contains Python modules for modeling and reconstruction of diffusion weighted MRI data. It is a subset of the code internally used in the CVGMI lab at the University of Florida. Three different reconstruction methods are currently included in this program, namely, Mixture of Wisharts (MOW), Diffusion Orientation Transform (DOT) and Q-ball Imaging (QBI).

This program is mainly developed and maintained by Bing Jian, as part of his Ph.D. research, supervised by Prof. Baba Vemuri.

Please note that the source code of this program is hosted at Google Code, see the "Source Code" link on the left.

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.
Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive ROI and VOI tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.

MoTrak - Head Motion Tracking System

Designed for use in an MRI simulator, MoTrak software uses Ascension Technology’s Flock of Birds. The sensor attaches to the subject’s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time, allowing observation of head motion in an MRI simulator.

In the simulator, the participant can simultaneously be habituated to the MRI environment, while being trained to remain still via feedback from the MoTrak system.

JIST: Java Image Science Toolkit

Java Image Science Toolkit (JIST) provides a native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces.

This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. To participate in this consortium or seek assistance in integrating JIST modules in your application, please contact us at jist-admin@www.nitrc.org.

JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).

cbiNifti: Matlab/Octave Nifti library

cbiNifti: An I/O library for Matlab/Octave

Matlab and Octave library for reading and writing Nifti-1 files.

cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data.

cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression.

More information and code examples at:

http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

Internet Brain Volume Database (IBVD)

The IBVD provides a web-based searchable database of brain neuroanatomic volumetric observations. This is designed to access both group volumetric results as well as volume observations in individual cases. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as meta-analysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses.

Neural ElectroMagnetic Ontologies

We first provide a NEMO_spatial ontology for the public to annotate their EEG/ERP data. The URL is:

http://aimlab.cs.uoregon.edu/NEMO/ontology/1.0/NEMO_spatial.obo

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). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.

Please note that package files and source code can be downloaded from TractoR's Google Code home page, via links on the left.

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. Babak A. Ardekani, Alvin H. Bachman, Model-based automatic detection of the anterior and posterior commissures on MRI scans, N
euroImage, Volume 46, Issue 3, 1 July 2009, Pages 677-682, ISSN 1053-8119, DOI: 10.1016/j.neuroimage.2009.02.030.
(http://www.sciencedirect.com/science/article/B6WNP-4VRP25C-4/2/8207b962a38aa83c822c6379bc43fe4c)

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. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion. Further information is available at http://www.crl.med.harvard.edu

E-Prime 2.0

E-Prime® is a suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime® provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime® provides millisecond precision timing to ensure the accuracy of your data. E-Prime’s flexibility to create simple to complex experiments is ideal for both novice and advanced users.

The E-Prime® suite of applications includes:
•E-Studio – Drag and drop graphical interface for experiment design
•E-Basic – Underlying scripting language of E-Prime
•E-Run – Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection.
•E-Merge – Merges your single session data files for group analysis
•E-DataAid – Data management utility
•E-Recovery – Recovers data files

dinifti

Convert DICOM images to NIfTI format.

MindSeer

MindSeer is a cross-platform application for 3D brain visualization. It is written in Java/Java3D, and runs in both standalone and client-server mode. Click on the MindSeer Project Page for downloads, tutorials, source code, demos and a publication.

Anatomist

Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/supress objects, change colors, draw regions of interests, do manual registration, etc.

BrainVISA

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developped for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.).

BrainVISA main features are:
- Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc.
- Ontology-based data organization allowing database sharing and automation of mass of data analysis.
- Fusion and interactive visualization of multimodal data (using Anatomist software).
- Automatic generation of graphical user interfaces.
- Workflow monitoring and data quality checking.
- Full customization possible.
- Runs on Linux, Mac and Windows.

SRI24 Atlas: Normal Adult Brain Anatomy

SRI24 is an MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects.

The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures.

The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.

As per the CC-BY-NC-ND license, please cite the following paper in publications using the SRI24 atlas:

T. Rohlfing, N. M. Zahr, E. V. Sullivan, and A. Pfefferbaum, “The SRI24 multichannel atlas of normal adult human brain structure,” Human Brain Mapping, vol. 31, no. 5, pp. 798-819, 2010. DOI: 10.1002/hbm.20906

An earlier paper is available at PMC:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2633114

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. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.

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.

The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear regression).

CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), CUDA (GPU), and MPI (distributed).

Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.

Journals

If you are seeking journals addressing functional and structural neuroimaging topics, this is the right place to start.

Books

If you are interested in finding books related to neuroscience, you have come to the right place! Books is a bibliography of books addressing the topic of functional and structural neuroimaging.

PST MRI Simulator

The Psychology Software Tools MRI Simulator provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness.

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. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings.

The key features include:

- NIfTI support for scalar, vector and DTI volumes

- tool chains for manipulating DTI volumes: resampling, smoothing, warping, registration & visualization

- pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies

- built-in cluster-computing support

- Interoperability with other major DTI tools: AFNI, Camino, DTIStudio & FSL

Brede Wiki

The Brede Wiki is a semantic wiki with structured information from neuroscience. It contains listing of results from neuroimaging studies such as Talairach coordinates and brain volume measurements as well as items for researchers, software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed.
Search on Talairach coordinates in the database is available from an external specialized search engine.

UNC - Pediatric Atlases

The pediatric atlases for neonates and one-year-olds were constructed at UNC-Chapel Hill using a dataset collected from one of our longitudinal studies, which involved 68 subjects with images acquired at neonatal onset and at one-year-old. A dedicated strategy based on longitudinal probability information was used to guide the segmentation of the images. Images were groupwisely registered to generate the atlases.

Please cite the following article for using the atlases:
"Neonatal brain image segmentation in longitudinal MRI studies", Neuroimage, 49(1):391-400, Jan 2010. [Feng Shi, Yong Fan, Songyuan Tang, John H. Gilmore, Weili Lin, Dinggang Shen]

For more information and download link, please visit:
http://bric.unc.edu/ideagroup/free-softwares/

fMRI-CPCA

Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline.

CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network.

fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated.

BRAINSCortex

This suite of tools will generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

CIGAL

CIGAL is a program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL’s real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables).

BXH/XCEDE Tools

A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts.

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. Through its edge preserving properties they reduce data noise without compromizing significant structures.

R-package for adaptive fMRI analysis

The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.

UNC Primate Brain Atlas

This symmetric atlas of the primate brain has been created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image (with and without skull), and also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures segmentation (amygdala, caudate, hippocampus, pallidus, putamen), and a lobar parcellation map.

You can find more details about the creation of this atlas in the following paper :
M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8

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).

The functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.

Installation notes and documentation are available at the official project page:

http://www.vmtk.org/Main/VmtkIn3DSlicer

WFU_Pipeline

The WFU SPM5 Pipeline is a fully automated method for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition.

Landman NeuroImaging Tools

Project to provide long-term hosting and release for small tools related to medical image analysis. Source repository contains highly experimental code intended for collaborative development. However, any interested parties are welcome to browse/reuse code. Stable/evolved projects will be moved to independent projects.

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).

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. DICOM Browser includes scripatable header editing to support various de-identification protocols. DICOM Browser is written in Java and uses ImageJ for image viewing and dcm4che toolkit for much of its DICOM implementation. For more information: http://nrg.wustl.edu/projects/DICOM/DicomBrowser.jsp

ProbabilisticBiasCorrection

A multichannel capable tool for probabilistic inhomogeneity correction implemented as both a standalone command line tool and a Slicer3 module.

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. MRI is used as surrogate imaging marker, as MRI signal changes reﬂect certain aspects of brain pathology.Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response.
The brain lesion segmentation tool uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation.
Primary Contact: Christos Davatzikos
Contributors: Zhiqiang Lao ,Dinggang Shen ,Eva Zacharaki,Nick Bryan

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. on Medical Imaging, 21(11):1421-1439, Nov 2002), an algorithm for elastic registration of medical images using geometric moment invariants as attributes and hierarchical attribute matching mechanism for finding deformation field. In this project, we will develop HAMMER registration module for 3DSlicer.

We will also develop a 3DSlicer module for white matter lesion (WML) segmentation. (Zhiqiang Lao, Dinggang Shen, Dengfeng Liu, Abbas F Jawad, Elias R Melhem, Lenore J Launer, Nick R Bryan, Christos Davatzikos, Computer-Assisted Segmentation of White Matter Lesions in 3D MR images, Using Pattern Recognition, Academic Radiology, 15(3):300-313, March 2008).

ARCTIC

ARCTIC (Automatic Regional Cortical ThICkness) is an end-to-end application developped at UNC-Chapel Hill allowing individual analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line.

xjView, a viewing tool for SPM

xjView is a viewing program for SPM2 and SPM5. p-value slider, displays multiple images at a time and can be used to build ROI masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, google scholar and pubmed).

Segmentation Validation Engine

The Segmentation Validation Engine (SVE) provides an automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site. Details on the methodology can be found in the following paper:

Shattuck DW, Prasad G, Mirza M, Narr KL, and Toga AW (in press) Online Resource for Validation of Brain Segmentation Algorithms NeuroImage, e-pub available online Nov. 25, 2008 (doi:10.1016/j.neuroimage.2008.10.066).

BRAINSMush

Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

3DSlicerLupusLesionModule

The purpose of this Slicer3 module is to provide a capability for performing white matter lesion classification and summary.

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. BrainMask implements a fully automatic brain segmentation algorithm that uses advanced "thresholding with morphology" and 3D edge detection algorithms. BrainMask demonstrates high segmentation accuracy. For a representative 26 datasets, the segmentation error averaged 3.4% ± 1.3% (Mikheev A et al. J Magn Reson Imag 27(6):1235-41;2008).

BrainMask includes NNN - a tool based on the algorithm developed by John Sled for correcting the intensity non-uniformity in MR data (Sled JG et al. IEEE Trans Med Imag 17(1):87-97;1998).

BrainMask also includes a versatile DICOM wiewer and allows to selectively load and organize DICOM images into 3D and 4D datasets.

Statistics Online Computational Resource

The Statistics Online Computational Resources (SOCR) include the following suite of web-based Java applets:
* Distributions (interactive graphs and calculators)
* Experiments (virtual computer-generated games and processes)
* Analyses (collection of common web-accessible tools for statistical data analysis)
* Games (interfaces and simulations to real-life processes)
* Modeler (tools for distribution, polynomial and spectral model-fitting and simulation)
* Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis),
* Additional Tools (other statistical tools and resources)
* SOCR Java-based Statistical Computing Libraries.

In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline).

INCF

The International Neuroinformatics Coordinating Facility (INCF) coordinates and fosters international activities for discovery in neuroscience and related fields. Established in 2005 through the Organisation for Economic Co-operation and Development (OECD) Global Science Forum, the INCF catalyzes global knowledge flow and scientific interaction by developing, maintaining and evaluating worldwide programs, standards, guidelines and infrastructures in neuroinformatics to further our understanding of the human brain and its diseases. With its Secretariat at the Karolinska Institutet and Royal Institute of Technology in Stockholm, Sweden, the INCF achieves its international outreach through national nodes in 14 member countries around the globe.

Mouse BIRN

The Mouse BIRN Testbed is helping scientists study neurodegenerative diseases by marshaling multi-modal data from the mouse, as an animal model, to investigate neurological disorders. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder.

Textpresso - literature search engine

Textpresso is a text-mining system for scientific literature. Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature.
Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 17 different literatures, among them Neuroscience, and can readily be extended to other corpora of text.
Textpresso can be used online (http://www.textpresso.org), but also installed
locally via a downloadable software package (http://www.textpresso.org/downloads.html)

POLGUI- Matlab GUI for Polhemus Fastrak

POLGUI is an interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations.

There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms),
1. polgui_ver1_r14 : works with 1 receiver (stylus pen)
2. polgui_ver2_r14 : works with 2 receivers (including the pen)
3. polgui_ver3_r14 : works with 3 receivers(including the pen)
4. polgui_ver4_r14 : works with 4 receivers (including the pen)
5. polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers [WARNING: Ver 5 might be buggy; not fully tested]

Requirements: MATLAB R14 (Linux/Windows)

BrainVoyager Brain Tutor

The free BrainVoyager Brain Tutor teaches you knowledge about the human brain through interactive exploration of rotatable 3D models. The models have been computed with BrainVoyager QX using original data from magnetic resonance imaging (MRI) scans. Besides having fun with the rotatable 3D models, the program contains information about the major lobes, gyri, sulci and Brodmann areas of the cerebral cortex.

BrainVoyager Viewer

BrainVoyager Brain Viewer allows to browse and inspect essential BrainVoyager data files. In addition, the program supports viewing the header and content of DICOM files. The Viewer also supports standard image files (JPEG, GIF, PNG, TIFF, BMP) allowing to inspect snapshots, figures or photos. The program offers an elegant user interface with fluid navigation abilities inspired by Apple's "Cover Flow" and the iPhone interface. The program can be downloaded and distributed freely.

N3 - MINC B0 nonuniformity correction

nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.

Level-set Segmentation for Slicer3

The modules in the framework support different tasks in the segmentation realization in 3DSlicer.

A module called Level-set label map evolver was developed, which takes an initial label image and a feature image as input and performs a Geodesic Active Contours evolution on the label image according to the feature image and to a different terms in the level-set equation. The evolution takes place for a customizable number of iterations.

The output is a label image that can be used to produce a model.

Other modules were developed to accompany the main module as can be seen in http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Level-Set_Segmentation_Framework-Documentation

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. This software includes MEG and EEG preprocessing tools, interactive and batch-mode modules for the forward and inverse calculations, as well as various data conditioning and data conversion utilities.

This is a subproject of the Center for Functional Neuroimaging Techniques (http://www.nitrc.org/projects/cfnt/)

JHU Proj. in Applied Medical Imaging

This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose.

Optseq - fMRI Event Scheduler

Optseq is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. RPER is also more efficient than fixed-interval event related (FIER) because more stimuli can be presented within a given scanning interval at the cost of assuming that the overlap in the hemodynamic responses will be linear. In SPM parlance, RPER is referred to as 'stochastic design'.

This is a subproject of the Center for Functional Neuroimaging Techniques (http://www.nitrc.org/projects/cfnt/)

Center for Functional Neuroimaging Tech

The Center for Functional Neuroimaging Technologies (CFNT) is a Regional Resource located at the Athinoula A. Martinos Center for Biomedical Imaging at the Massachusetts General Hospital. The primary mission of the Center is to expand understanding of the human brain in health and disease through the development and dissemination of innovative multimodal Magnetic Resonance (MR)-based neuroimaging techniques and technologies. The Resource is sponsored by the National Center for Research Resources of the NIH.

BRAINSCut

BRAINSCut is a software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper "Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures." [PMID: 17904870]. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

Neuroinformatics - The Journal

Neuroinformatics publishes original articles and reviews with an emphasis on data structure and software tools related to analysis, modeling, integration, and sharing in all areas of neuroscience research. Coverage extends to theory and methodology, including discussions on ontologies, modeling approaches, database design, and meta-analyses; descriptions of developed databases and software tools, and of the methods for their distribution; relevant experimental results, such as reports accompanied by the release of massive data sets; computational simulations of models integrating and organizing complex data; and neuroengineering approaches, including hardware, robotics, and information theory studies. Neuroinformatics also publishes independent "tests and evaluations" of available neuroscience databases and software tools, and fosters a commitment to the principles of tool and data sharing.

PyMVPA

PyMVPA is a Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. 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.

DSI Studio

DSI Studio is a software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. http://dsi-studio.labsolver.org

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.

NeuroWeb - NeuroImaging Database

NeuroWeb provides infrastructure for data aggregation, processing, and management in multi-dimensional medical imaging research (i.e., MRI, CT, PET). NeuroWeb is designed for rapid deployment on a small/moderate scale with limited hardware.

Maps4Mipav (Exploratory JIST)

Java Image Science Toolkit (JIST) is an extension to the MIPAV (Medical Image Processing, Analysis, and Visualization) plug-in framework that allows the user to design and execute pipelines, which are multi-stage processing tasks.

JIST was formerly known as the MedIC Automated Pipeline Scheduler (MAPS).

This is the exploratory development tree. New features and designs are tested here before general release into the JIST project.

Access to the source code is freely given. However, registration is required so that we can notify users of critical changes. For unrestricted access to the stable release, see the JIST project. http://www.nitrc.org/projects/jist/

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). MedINRIA is intended to be used by anyone curious about medical images!

DW-MRI Random Walk Simulator

The DW-MRI Random Walk Simulator provides a simple interface to simulate Brownian motion in arbitrary, complex environments. The analysis routines enable visualization of these models with DTI, q-space, and higher order diffusion weighted MRI..

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. Jim is an up-to-the-minute design with a familiar user-interface.

ODIN

ODIN is a C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

MRIcron

MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics. MRIcroGL is a variant of MRIcron that uses OpenGL for very fast rendering, but requires a modern NVidia or ATI graphics card.

BRAINSDemonWarp

BrainDemonsWarp is a command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library.

This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

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.

BrainMaps.org

BrainMaps.org is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains.

CoCoMac Brain Connectivity Database

CoCoMac.org gives online access (html or xml) to structural connectivity ('wiring') data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies.

Conferences, Workshops and Meetings

This project assists the community in the collection and dissemination information about upcoming Conferences, Workshops and Meetings. All users are encouraged to check this site for upcoming meetings, and promote future meetings here.

Insight Toolkit

The ITK toolkit is based on generic programming, with a data pipeline architecture, supports for multi-threads, and it is tested Nightly in multiple platforms including Linux, Windows, Sun and Mac.

PubBrain Database

PubBrain is a literature search and visualization tool that allows end users to enter any PubMed query and see that query rendered as a heatmap illustrating which regions of interest are most commonly mentioned within the search results.

JIST Resources for Algorithm Development

This repository stores plugins, tutorial code, and examples demonstrating MRI manipulation within the MIPAV plugin environment.

This project is separate from JIST so that we can provide WRITE access to any interested party without overly exposing the infrastructure to unplanned modification. Please contact the administrators if you would like to join this project - open use is encouraged.

SumsDB Database

SumsDB is a repository of neuroimaging data (surfaces & volumes; structural & functional data), mainly from humans and macaques but also mouse, rat, and great apes. WebCaret is an online visualization tool for viewing SumsDB datasets. Visit the Tool/Resource Home Page for more information.

BRAINSTracer

BRAINSTracer - a graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme.

map3d

map3d supports interactive visualization of surface based time signals such as high resolution EEG, MEG, and ECG.

Seg3D

Seg3D is a free volume processing sgementing tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.

cmrep

The continuous medial representation (cm-rep) is a set of deformable modeling algorithms for shape analysis and structure-specific normalization. Applications of cm-reps include structure-specific fMRI analysis, DTI analysis, and structural brain mor

DICOM_UploadGUI

UploadGUI is a Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr

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. Its primary use is to enable the testing of tracking algorithms

VectorValuedHistogramNormalizer

Implement the methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf as and ITK filter.

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). Designed for neuroscience and medical imaging researchers and users. Special capabilities include symmetric diffeomorphic normalization, optimal template creation and user-guided normalization.

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.

There are also a number of tools including Registration and Non-Uniformity correction.

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.

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. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span.
These tools are distributed in the form of plugins for a popular analysis package BrainVisa

ITools Resourceome

iTools is an infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

iBrain™

iBrain™ is an easy-to-use processing and visualisation platform designed to explore functional fMRI and other neuroimaging data. iBrain™ can be used stand-alone, or in conjunction with other analysis packages (e.g. SPM).

fMRIstat

A Matlab toolbox for the statistical analysis of fMRI data.

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.

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.

XCEDE Schema

The XML-Based Clinical Experiment Data Exchange Schema provides an extensive metadata hierarchy for describing and documenting research and clinical studies. XCEDE was originally designed in the context of neuroimaging studies and complements the BIRN-HID

Diffusion Toolkit / TrackVis

Diffusion Toolkit (with TrackVis) is a cross-platform software package that does reconstruction, fiber tracking, visualization and analysis on various diffusion imaging data. Features of the software include:

• Handles DTI, DSI, Q-Ball and HARDI imaging techniques.
• Works on Windows, Mac OS X and Linux with native look and feel. Native 64-bit support on Mac OS X and Linux.
• Fast streamlined data processing.
• Intuitive GUI front-end with command-line driven back-end. Thus, allows advanced user to write their own scripts for automated multiple dataset processing.
• Real-time fiber track visualization and analysis. Parameter adjustment applied to 3D render on the fly. Various tracking selection methods (filters) allows locating specific track bundle with ease.

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.

ITK-SNAP

ITK-SNAP is an open-source software application for medical image segmentation. Its primary use is for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data. ITK-SNAP is actively developed by Paul Yushkevich, Hui Zhang, and colleagues at the Penn Image Computing and Science Laboratory at the University of Pennsylvania.

Penn Hippocampus Atlas

The Penn Hippocampus Atlas is a resource consisting of segmented and normalized high-resolution postmortem MRI of the human hippocampus. The atlas is described in Yushkevich et al., A high-resolution computational atlas of the human hippocampus from postmortem magnetic resonance imaging at 9.4 T, Neuroimage 44(2):385-398, 2009.

Data can be accessed using the SCM link on this page.

BASH4RfMRI

BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). I do not update this package, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts.

Brainscape

Brainscape is a database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal.

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.

Artifact Detection Tools (ART)

Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well.

Biomedical Informatics Research Network

BIRN is a geographically distributed virtual community of shared resources to advance the diagnosis and treatment of disease.

Diffusion Warp

This project contains tools appropriate for the registration of diffusion tensor images to an average coordinate system. The tools include image registration methods and algorithms for the correct alignment of the diffusion tensor when applying the resulting transformation. The program uses the Slicer3 execution model framework to define the command line arguments, and can be fully integrated using the module discovery capabilities of Slicer3.

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

Mango

Mango is a medical image viewer for Windows, Mac OS X, Unix, Linux, and Web platforms. It provides tools to analyze images and an interface to navigate the image volume.

* Built-in support for NIFTI, Analyze, NEMA, and DICOM formats
* Customizable: Create custom filters, color tables, file formats, and atlases
* Extensible: Supports plugin development using the Mango Plugin API
* Web: Create interactive images on a web page using the Mango applet

* ROI Editing: Threshold and component-based tools for creating, painting, and tracing ROIs
* Surface Rendering: Interactive surface models supporting cut planes and overlays
* Image Registration: Semi-automatic image coregistration and manual image transform editing
* Image Stacking: Threshold and transparency-based image overlay stacking
* Analysis: Histogram, cross-section, time-series analysis, image and ROI statistics
* Processing: Kernel and rank filtering, arithmetic/logic image and ROI calculators

Homepage: http://ric.uthscsa.edu/mango/

Lumina LP- 400 Response System

The Lumina LP-400 is a reliable patient response system designed specifically for use in an fMRI. Lumina was developed to satisfy the requirements of both the clinical and research fields.

NIH Pediatric MRI Data Repository

The NIH Pediatric MRI Data Repository contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

BrainCSI

BrainCSI is a tool for partial volume correction in CSI data. This program is built upon the NA-MIC toolkit and is intended to interface with Slicer3.

BRAINSTestData

The BRAINS suite of tools (BRAINSFit, GTRACT, BRAINS, BRAINSTracer... and others) use a common set of anonymized data for nightly regression testing. This data is about 1.2GB of anonymized imaging data of many different file formats used to ensure t

MRI Studio

MRI and DTI imaging software tool.

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. This correction improves test-retest reproducibility crucial for multi-site studies.

IDeA Lab brain image processing suite

Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added.

Functional Connectivity Community

The purpose of this project is to provide a community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc.

Automatic Registration Toolbox

Automatic detection of the AC and PC landmarks on 3D structural MRI scans.
Linear and non-linear registration algorithms for matching brain images between and within subjects and imaging modalities. Applications include inter-subject registration of 3D MRI, MRI-PET/SPECT registration, and EPI spatial distortion correction.

LDDMM

LDDMM assigns a metric distances on the space of anatomical images

MIView

MIview is an OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

BrainGraph Editor 1.0 Beta

The BrainGraph Editor 1.0 Beta is a JAVA application designed to create taxonomies or hierarchies in order to classify and organize information.

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. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it’s plugin architecture.

MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display:

Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches.

Registration Workspace: performs 2D landmark based registration.

Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware.

Atlas Viewer: allows navigation and interrogation of volumetric atlases.

Hierarchy Editor: create logical groupings of atlas labels.

Task Independent Fluctuations Discussion

The methodology and applications of task independent fluctuation measures including: connectivity maps of fMRI resting state scans, research using EEG/MEG/PET etc, methods to remove non-neural fluctuations, and applications to clinical populations.

Slicer3 Example Modules

Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation.

MPScope

MPScope is a comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, the analysis program MPView and several software utilities

Human Imaging Database (HID)

The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.

Grantees Meeting for NITRC

This project is meant for planning the NITRC Grantee meetings. The meetings introduce NITRC participants to one another, promote discussion of common interests, and identify opportunities for collaboration and interoperability.

Plans for the 2009 Grantee Meeting are underway. Click on the MediaWiki link (in gray menu on left) to learn more.

NPTK

NPTK provides non-rigid registration/distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.

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.

GTRACT

GTRACT is a Diffusion Tensor fiber tracking suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

GIFTI

Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI).

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.

VoxBo

VoxBo is a highly modular and interoperable collection of free tools for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages.

Stochastic Tractography System

Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images. This project provides tools which can perform Stochastic Tractography and related analysis on DWMRI data.

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.

Slicer3 Module Rician noise filter

Two Slicer3 modules removing rician noise in diffusion tensor MRI

BVQXtools

BVQXtools is a Matlab-based toolbox for the reading, writing, and processing of BrainVoyager (QX) files in Matlab. The toolbox is freely available.

HAMMER: Deformable Registration

The HAMMER package performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.

FSL extensions

FSL extensions is a reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL).

NVM

NVM is an open-source software tool for locating and measuring neuroanatomy in structural volumetric image data. It is used to draw regions of interest for subsequent fMRI analysis.

Functional Imaging BIRN

The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets.

NeuroLens

NeuroLens is an integrated environment for the analysis and visualization of functional neuroimages.

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.

XNAT

XNAT is an open source imaging informatics platform designed to facilitate management and exploration of medical imaging and related data. XNAT includes a DICOM workflow, a secure database backend, and a rich web-based user interface. XNAT's web services interface enables external applications to easily access XNAT-hosted data.

Morphometry BIRN

The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focuses on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer’s disease.

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. An alpha-release is currently available for use with an example dataset and tutorial.

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.

Talairach Daemon

The Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach atlas.

BrainMap Database

BrainMap is a community database of published functional neuroimaging studies (mainly PET and fMRI). BrainMap contains both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates.

BRAINSFit

A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

BioImage Suite

BioImage Suite is a general purpose registration/segmentation/visualization suite. It also has facilities for DTI and fMRI processing.

3D Slicer

An extensible, cross-platform, totally open research platform for image computing.

IATR

The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community.

IBSR

The Internet Brain Segmentation Repository (IBSR) provides manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the evaluation and development of segmentation methods.

WFU_BPM

The WFU Biological Parametric Mapping (WFU_BPM) toolbox performs SPM analysis with voxel-wise imaging covariates.

WFU_PickAtlas

WFU_PickAtlas provides a method for generating ROI masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label and Tissue Type.

LONI Inspector

The LONI Inspector is an application for examining medical image files. The Inspector focuses on reading, displaying, searching, comparing, and exporting "metadata" (e.g., patient name, the model of scanner).

LONI De-identification Debablet

The LONI de-identification Debablet is an application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.

LONI Debabeler

The LONI Debabeler manages the conversion of imaging data from one file format and convention to another. It consists of a GUI to visually program the translations, and a data translation engine to read, sort and translate the input files.

BrainFX

A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA's and Brainwaver's User interface.

Brainwaver

Characterisation of small-world networks constructed from wavelet analysis of resting fMRI. This package is currently available as an R library. Futrure development will take place within the CamBA software repository

CamBA

Software respository containing pipelines of chained modules and GUI for batch processing. Current pipelines include fMRI analysis, statistical testing based on randomisation methods and fractal spectral analysis. Pipelines are continually being added.

MEG Tools

MEG Localization using FOCUSS and MR-FOCUSS

FMRIpower

A common question investigators ask statisticians when working on grants is how to calculate power. FMRIpower is an easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data.

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.

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. Visit the Tool/Resource Home Page for more information.

Mindboggle: automated brain labeling

Mindboggle automates anatomical labeling of human brain MR data. The present beta version is written in Matlab; a new version is under development. More information may be obtained from http://www.mindboggle.info

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. Visit http://pipeline.loni.ucla.edu for more info.

FIV

The Functional Image Viewer, also known as FIV, is a tool for visualizing functional and anatomic MRI data.

NIfTI

The Neuroimaging Informatics Technology Initiative (NIfTI) and NIfTI Data Format Working Group, creator and maintainer of the NIfTI-1 data format.

FSL

FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK.

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, EEG and MEG.

AFNI

AFNI is a set of C programs for processing, analyzing, and displaying FMRI data. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free for research purposes.

Resource Ontology Discussion Group

This project will discuss, debate, develop and deploy ontological practices for the fMRI community.

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.

NITRC Community

This resource provides NITRC-wide facilities: Forums, Wiki, Tracker, and News.