Tool/Resource Listing

Brain Vision Analyzer

Since 1997, BrainVision Analyzer has made its way into thousands of research labs, helping scientists to manage their daily work of analyzing various neurophysiological data. Thanks to its ease of use, the handling of an amazing number of powerful features is just a snap. The editable History Tree® lets you organize, explore and trace evaluation steps. Automated analysis with drag & drop functions speeds up recurring tasks. Various data format readers recognize files from different EEG manufacturers automatically and guarantee compatibility and exchangeability with research labs all over the world. The Analyzer includes all necessary pre-processing functions, enhanced time-frequency analysis options, ICA, LORETA, MRI correction as well as a direct interface to MATLAB ®. New views create unlimited output possibilities to publish your results. Programming interfaces in .NET languages can be used to expand functionality.

Micro-Manager

Micro-Manager (http://micro-manager.org) operates motorized light microscopes and associated equipment. It runs as a plugin in ImageJ, works with virtually all scientific grade microscope equipment, and has a simple interface towards routine image acquisition strategies such as time-lapse, z- stacks, multi-channel, and multi-position acquisition. In addition, it uses a device abstraction layer available from various programming environments (such a C, Java, Python, Matlab and LabView), facilitating development of novel approaches to image acquisition.

imcalc: SPM batch image calulator

"imcalc" is an image calculator with batch functionality for SPM5/SPM8.

Options:
[1] binarize non-zero voxels;
[2] binarize each image to a unique threshold;
[3] binarize each image to a unique threshold, then sum;
[4] binarize non-zero voxels, then sum;
[5] binarize non-zero voxels, sum, rebinarize;
[6] pairwise operation (add sub mult div ... etc.);
[7] flip sign of all non-zero voxels;
[8] flip image along x-axis;
[9] mask images to a template;
[10] T-to-Z transform;
[11] cap positive/negative values.

For a screenshot, visit http://tools.robjellis.net

INVIZIAN

Fly through and interact with hundreds of human brains to compare structural differences or carefully inspect individual specimens. Introducing the “Informatics Visualization in Neuroimaging (Invizian©)” Project, a 21st century visualization environment that enables you, via your computer, to display and interact with hundreds of neuroimaging data sets at once —bringing together brain image data from some of the world’s best neuroscience research teams. Invizian© empowers both researchers and students of neuroscience to explore and understand the human brain using Invizian’s© simple and powerful user interface for neuroimaging data exploration and discovery. Come back often to see how we are making continuing progress to make Invizian© even more amazing.

SINOMO (SIngular NOde MOtifs)

Network nodes can be described by node-motifs--a combination of local network features. Certain node-motifs, such as highly connected nodes or hubs, have been shown to be important components of networks. Costa et al. (2009) have presented a technique to detect and specify more complex compound motifs, which are characterised by multiple features in combination. We described improvements to that method and showed how its parameters can be determined automatically [Echtermeyer et al. 2011]. SIMONO is our implementation of the enhanced workflow, which can be controlled via a graphical user interface or through the command-line for batch processing.

Documentation is available at:
http://www.biological-networks.org/p/sinomo/
You can also directly download the Matlab/Octave code following the link below.

References:
* L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009
* C. Echtermeyer, L. Da Fontoura Costa, F. A. Rodrigues, M. Kaiser, PLoS ONE 6, 9, 2011

NFT: Neuroelectromag Forward Modeling

Neuroelectromagnetic Forward Head Modeling Toolbox (NFT) (http://sccn.ucsd.edu/nft) is a MATLAB Toolbox for generating realistic head models from available data (MRI and/or electrode locations), for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) and Finite Element Method (FEM) are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line. The toolbox is freely available under the GNU Public License for noncommercial use and open source development.

peak_nii

peak_nii: Statistical image clustering, peak detection and data extraction.
The Peak_nii toolbox was developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command.

vis: SPM Visualized Statistics toolbox

A simple, menu-driven toolbox for SPM software that provides the user with several options: (1) a histogram of all non-zero voxel values in an brain image; (2) a scatter plot, quantile-quantile plot, or Bland-Altman plot of statistic values at all corresponding voxel locations in two brain images; (3) a surface plot of all voxel values at a particular axial slice.

Note: the toolbox calls various SPM functions, and also makes use of several functions within the MATLAB "stats" toolbox. Both SPM (either 5 or 8) and the stats toolbox should be installed.

For further information and documentation, visit http://tools.robjellis.net

Measure Projection Toolbox (MPT)

This toolbox is an EEGLAB plugin for performing Measure Projection Analysis.

Measure Projection Analysis (MPA) is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component (IC) clustering issues by abandoning the notion of distinct IC clusters. Instead, it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects and/or sessions as quantified by the values of various EEG measures.

Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences.

BCILAB

BCILAB is a MATLAB toolbox for Brain-Computer Interface (BCI) research. It facilitates the design and development of new methods for cognitive state estimation and their use in both offline data analysis and real-time applications. BCILAB includes an easily extensible collection of currently over 100 methods from the literature (covering signal processing, machine learning and BCI-specific methods). Aside from supporting advanced BCI research, a special aim of BCILAB is to facilitate the adoption of machine learning and advanced statistical modeling for functional neuroimaging purposes in tandem with the EEGLAB platform.

Solar Eclipse Imaging Genetics tools

The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Thus we are developing software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing.

Our focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data

BioSig

Biosig provides tools for processing of electroencephalogram (EEG) and other biomedical signals like ECG, EOG, EMG, etc. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis.

Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided.

Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis.

It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.

Neuroimaging Made Easy Blog

The main aim of this blog is presenting some scripts that can be used to facilitate and automate processing and analysis of brain data. In addition, it could be helpful explaining non clear stages and steps of brain data processing using some software.

EEProbe

EEProbe is a complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser.

ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities.

All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats.

Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis.

EEProbe is available for Linux and Mac OS X.
www.ant-neuro.com

ASA - Advanced Source Analysis

ASA is a highly flexible EEG/ERP and MEG analysis package with a variety of source reconstruction, signal analysis and MRI processing features. ASA combines functional brain imaging with the visualization and incorporation of morphological information obtained from MRI or CT. ASA is a highly interactive and flexible software tool that can be applied to neuro-physiological and clinical brain research.

ASA gives a realistic impression of your experimental configuration together with topographical mapping of EEG and MEG and the results of your analysis. ASA is developed for and by people dedicated to brain research. The concept of flexibility and openness covers even most complex analysis demands. The ASA environment is particularly attractive for those that wish to develop their own methods in third party packages like Matlab and use ASA for pre-processing and visualization purposes.

LIBEEP

The LIBEEP library deals with reading and writing RIFF-format CNT/AVR-files.

This file format is also called "EEProbe data format", and is used in the software packages EEProbe, ASA, ASA-Lab, Cognitrace, eemagine EEG, Visor, by ANT Neuro B.V., The Netherlands.

The file format provides for storage of EEG/ERP/MEG data as 32-bit values, and includes a very efficient compression algorithm. Encoding/decoding from the compressed data is performed automatically through the LIBEEP interface functions.

ParaView

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Net Station

APIs for Net Station data files. APIs are available for C++, C#, and Java.

Source Information Flow Toolbox

The Source Information Flow Toolbox (SIFT) is an GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location.

Brain Segmentation Testing Protocol

The Brain Segmentation Testing Protocol (Neuroimage 2011, http://dx.doi.org/10.1016/j.neuroimage.2011.06.080) is a freely available collection of MRI images for testing segmentation algorithms. The 312 MRI datasets may be downloaded to assess the accuracy, reproducibility and sensitivity of MRI segmentation software. The accuracy/validation dataset includes images from infants, adults and patients with Alzheimer’s disease and the reproducibility dataset includes 9 subjects who have been scanned with 8 different sequences at 1.0T and 3.0T.

ALVIN - Lateral Ventricle Segmentation

ALVIN - Automatic Lateral Ventricle delIneatioN is a fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject. Download from here or visit our main website http://sites.google.com/site/mrilateralventricle/

TumorSim

TumorSim is a cross-platform simulation software that generates pathological ground truth from a healthy ground truth (e.g., the BrainWeb data). The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc). Example output simulation images are available for download for validating various image analysis algorithms such as registration and segmentation algorithms.

The simulation method is described in the following paper:
Marcel Prastawa, Elizabeth Bullitt, and Guido Gerig. Simulation of Brain Tumors in MR Images for Evaluation of Segmentation Efficacy. Medical Image Analysis (MedIA), Vol 13, No 2, April 2009, Pages 297-311.

MazeSuite

MazeSuite is a complete set of tools that enables researchers to perform spatial and navigational behavior experiments within interactive, easy to create, and extendable (e.g., multiple rooms) 3D virtual environments. MazeSuite can be used to design/edit adapted 3D environments where subjects’ behavioral performance can be tracked. MazeSuite consists of three main applications; an editing program to create and alter maps (MazeMaker), a visualization/rendering module (MazeWalker), and finally an analysis/mapping tool (MazeAnalyzer). Additionally, MazeSuite has the capabilities of sending signal pulses to physiological recording devices using standard computer ports. MazeSuite, with all 3 applications, is a unique and complete toolset for researchers who want to easily and rapidly deploy interactive 3D environments. For more information and related publications please see www.mazesuite.com

AMILab

AMILab is an opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK.

LORIS

LORIS is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: from heterogeneous data acquisition (imaging, clinical, behavior, genetics) to storage, processing and ultimately dissemination.

ERPLAB

ERPLAB Toolbox is a set of open source, freely available Matlab routines for analyzing ERP data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH.

LIBRA

LIBRA is a toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. The software is developed by the IDEA group at the University of North Carolina at Chapel Hill, directed by Dr. Dinggang Shen(dinggang_shen@med.unc.edu).

Linux operating system is required for the stand-alone executable software. The graphical user interfaces and overall framework of the LIBRA software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

UNC Human DTI Brain Atlas

Human DTI brain atlases have been generated at UNC-Chapel Hill for several age groups, by iterative joint deformable registration of training datasets into a single unbiased DTI average image. Atlases packages include an atlas DTI tensor image, atlas DTI property images (FA, MD, AD, RD), and single tensor tractography based fiber tracts of major tracts with related 3D planes for fiber profile information: genu, splenium, anterior and posterior limb of internal capsule, uncinate fasciculus.

MEGSIM

MEGSIM, http://cobre.mrn.org/megsim/, contains realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity.

Microstructural correlation toolbox

Microstructural correlation toolbox (MSC) is a Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS.
The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects. Please refer to the following publication for detailed information:
Li YO, et al., "Independent component analysis of DTI reveals multivariate microstructural correlations of white matter in the human brain", Hum Brain Mapp.2011.

EEGLAB

EEGLAB is to date the most popular EEG/MEG/ECoG software with about 100,000 download worldwide since 2003. EEGLAB provides an interactive graphic user interface (GUI) 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, as well as standard averaging methods. EEGLAB also incorporates extensive tutorial and help windows, plus a command history function that eases users' transition from GUI-based data exploration to building and running batch or custom data analysis scripts. EEGLAB offers a wealth of methods for visualizing and modeling event-related brain dynamics, both at the level of individual EEGLAB 'datasets' and/or across a collection of datasets brought together in an EEGLAB 'studyset.' For experienced Matlab users, EEGLAB offers a structured programming environment for storing, accessing, measuring, manipulating and visualizing event-related EEG data.

DTI-Reg

DTI-Reg is an open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration.

Individual steps of the pair-wise registration pipeline are performed via external applications - some of them being 3D Slicer modules. Starting with two input DTI images, scalar FA maps are generated via dtiprocess. Registration is then performed between these FA maps, via BRAINSFit/BRAINSDemonWarp or ANTS -Advanced Normalization Tools-, which provide different registration schemes: rigid, affine, BSpline, diffeomorphic, logDemons. The final deformation is then applied to the source DTI image via ResampleDTI.

FiberViewerLight

Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm.
As in the full version you can also display a plane on the fiber.
This tool works faster than the full version due to simplified visualizations.

BPM Accounting for Random Regressors

Biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. Current statistical methods in the imaging community assume that the regressors are non-random. For more realistic multi-parametric assessment (e.g., voxel-wise modeling), distributional consideration of all observations is appropriate. Herein, we present two unified regression and inference approaches, Model II regression and regression calibration, for use in massively univariate inference with imaging data. These methods use the design matrix paradigm and account for both random and non-random imaging regressors.

DPARSF

Data Processing Assistant for Resting-State fMRI (DPARSF) is a convenient plug-in software based on SPM and REST. You just need to arrange your DICOM files, and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data, FC, ReHo, ALFF and fALFF results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. You can use DPARSF to extract AAL or ROI time courses (or extract Gray Matter Volume of AAL regions, command line only) efficiently if you want to perform small-world analysis.

Please download it and find more information from http://www.restfmri.net/forum/DPARSF

Create DWI Atlas

This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWI's. The modules included are:

1) A Groupwise Registration module -> compute's a deformation field for each DWI, using, for example, FA maps as input
2) Warp DWI module -> used to warp each DWI using the deformation from (1)
3) DWI Averager -> used to average the set of warped DWI's producing the final DWI Atlas

Fiber Tracking Tool

Used to analyze the fibers produced by ukf tractography

3d Brain Atlas Reconstructor

3d Brain Atlas Reconstructor (3dBAR, http://www.3dbar.org) is a software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow.

3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets:

- downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings,
- previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures,
- downloading slides from available datasets as SVG drawings.

3dBAR service can also be used by other websites or applications to enhance their functionality.

Check http://www.3dbar.org for detailed description of the software and the latest releases.

CMFreg

We have developed a sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a “stable structure of reference” can be used without the simple “best fit” of all surfaces.

M3

The M3 (multi-modal imaging and multi-level characteristic with multi-classifier) is a brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.

Laboratory of Neuro Imaging (LONI)

The Laboratory of Neuro Imaging strives to improve our understanding of the brain in health and disease. LONI develops advanced computational algorithms and scientific approaches for the comprehensive and quantitative mapping of brain structure and function. LONI aims to encourage communication between users and LONI software engineers in order to improve the effectiveness of computational brain mapping software and to promote its use by researchers worldwide. LONI software website (http://www.loni.ucla.edu/Software/) includes downloadable and web-accessible tools, training and support. Be sure to visit LONI Forums and discuss our tools with other end-users and LONI investigators.

http://www.loni.ucla.edu

XNAT Extras

User contributions for XNAT.

BrainDecoderToolbox

Brain Decoder Toolbox performs “decoding” of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results.

BDTB is a set of Matlab functions.
BDTB is OS-independent.

UCLA Multimodal Connectivity Database

The UCLA Multimodal Connectivity Database - http://umcd.humanconnectomeproject.org - is a web-based analysis site and data repository for connectivity matrices that have been derived from neuroimaging data. The site is powered by the MGH/UCLA Human Connectome Project. Anyone can browse and analyze connectivity matrices that researchers have shared on this site. The data comes from different imaging modalities (fMRI, DTI, structural MRI, EEG), subject groups, and studies. The website allows users to choose any network shared by another user, compute graph theoretical metrics on the fly, and visualize the results.

Fast Nonlocal Means for MRI denoising

This is a fast and robust implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image.

It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images.

We use a bias correction step for Rician noise based on the well-known Conventional Approach.

This software can be compiled either as a Slicer module or a stand-alone:

http://www.nitrc.org/snapshots.php?group_id=518

Key words: nonlocal (non-local) means, NLM, C++, ITK

PySurfer

PySurfer is a Python based program for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi’s powerful visualization engine with a high-level interface for working with MRI and MEG data. PySurfer offers both a command-line interface designed to broadly replicate Freesurfer’s Tksurfer program as well as a Python library for writing scripts to efficiently explore complex datasets.

iBrain™ analysis toolbox for SPM

The iBrain analysis toolbox for SPM is a free toolbox that provides an automated processing pipeline for various single- or multi- subject and/or multi-session functional neuroimaging experiments. The pipeline includes image conversion from scanner-specific formats, pre-processing, statistical analysis, region-of-interest analysis, and display. It is possible to specify a complete analysis stream in advance (i.e. before any processing is actually performed). Analysis paradigms supported include block-design, event-related, simultaneous EEG/fMRI, and functional connectivity.

This toolbox is compatible with SPM2, SPM5 and SPM8.

scikit-learn

scikit-learn: machine learning in Python

OpenMEEG

A C++ package for low-frequency bio-electromagnetism
solving forward problems in the field of EEG and MEG with very high accuracy.

Wavelet-based Image Fusion

This is a Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2011).

OpenFMRI

OpenFMRI is a data sharing resource for task-based fMRI data. It aims to provide a resource for any fMRI researcher who wishes to share their data openly. Currently it provides access to raw fMRI datasets along with associated metadata. In the future, it will also provide access to processed datasets.

NeuroSynth

The NeuroSynth framework includes software tools for automated extraction and synthesis of data from published functional neuroimaging studies, a series of datasets generated using these tools, and a website (http://neurosynth.org) for visualizing and accessing many of the tools and results.

LIMO EEG

LIMO EEG is a matlab toolbox (EEGlab compatible) allowing the processing of
MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with our tool. Across subject analyses are performed using bootstrap offering robust inferences.

Licensing

Licensing issues in software and data.

All are invited to participate or join the project and contribute.

BrainNet Viewer

BrainNet Viewer is a brain network visualization tool, which can help researchers to visualize structural and functional connectivity patterns from different levels in a quick, easy, and flexible way.

connectir

Connectir is an R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity.

Please see our web page for more details: http://connectir.projects.nitrc.org or click the Home Page link on the right below.

MNI Macaque Atlases

We present unbiased standard macaque monkey magnetic resonance imaging template brain volumes that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual nonhuman primates and studies.

Brainsight

Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications.

NordicNeuroLab

With over a decade of experience, NordicNeuroLab (NNL) provides products and solutions that define the field of functional MR imaging. We understand the growing need for reliable and innovative tools in this growing field. As a result, we closely collaborate with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors to develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users.

From state of the art post-processing and visualization software for BOLD, Diffusion/DTI, and Perfusion/DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, NNL's products are used around the world by researchers and clinicians alike. Ultimately, we are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement.

NIRx NIRS Neuroimaging

NIRx Medical Technologies, LLC. is a leader in providing integrated solutions for NIRS neuroimaging.
We provide custom technology solutions to the investigative community for a wide range of NIRS imaging applications. While many of our systems are in the field of neuroscience (infants to adults), they are also used for investigation of breast cancer, peripheral vascular disease and the study of small animals.

DATAPixx

The DATAPixx is a complete multi-function data and video processing USB peripheral for vision research. In addition to a dual-display video processor, the DATAPixx includes an array of peripherals which often need to be synchronized to video during an experiment, including a stereo audio stimulator, a button box port for precise reaction-time measurement, triggers for electrophysiology equipment, and even a complete analog I/O subsystem. Because we implemented the video controller and peripheral control on the same circuit board, you can now successfully synchronize all of your subject I/O to video refresh with microsecond precision.

Hitachi Optical Topography System

Hitachi Medical Corporation is a leader in fNIRS neuroimaging with more than 10 years of experience. We provide researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience.

Data Format Tools

DFT is a loose collection of programs and configuration options that intend to make working with data more transparent to formats.

Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand.

Mag Design and Engineering

Mag Design and Engineering sells a variety of MEG- and fMRI-compatible hardware for research use. These items include typical response collection devices such as joysticks, response pads, mice, as well as stimulation devices such as vibrotactile stimulators, olfactometers, and pressure/force generators. The company also offers custom design and production services for many different applications.

fNIR Devices

fNIR Imager 1100 is a new generation portable functional near-infrared (fNIR) imaging research tool capable of monitoring brain’s hemodynamics and thereby the cognitive state of the subject in natural environments.

Neuroimaging Solution for Natural Environments:
• fNIR is the only stand-alone and field-deployable technology able to determine localized brain activity.
• fNIR can be readily integrated with other physiological and neurobehavioral measures that assess human brain activity, including eye tracking, pupil reflex, respiration and electrodermal activity. fNIR can also complement other techniques.
• Studies have shown a positive correlation between a participant's performance and fNIR responses as a function of task load.
• It has also been shown that fNIR can effectively monitor attention and working memory in real-life situations.

SR Research EyeLink Eye Trackers

SR Research, makers of the world leading EyeLink High-Speed eye tracker line, have been developing advanced eye tracking technologies and serving world class support to our research user base since 1992. The EyeLink line provides eye tracking capabilities for behavioral labs as well as for MRI, MEG, and EEG environments.

OEI fMRI compatible olfactometer

The OEI OLFACT-fMRI olfactometer is a computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive/learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory.

Fiber-tracking based on Finsler distance

This module uses the output of the "Finsler tractography" to actually trace the estimated fiber bundles from a set of target regions to the seeding regions used to compute the Finsler distance map. The map of optimal arrival directions is integrated with a second order Runge-Kutta method starting at the target regions and until the seeding region is reached (or some other stopping criterion is met).

Note that you should have "Finsler Tractography based on HARDI" installed and working in order to be able to use the present module (see the documentation therein for more details on the Finsler Tractography method).

This software can be compiled either as a 3D-Slicer CLI module or a stand-alone program (you need ITK and VTK). In the latter case, the fibers are written to disk.

NOTE: This software is currently provided as a sub-project in the Finsler-tractography module: http://www.nitrc.org/projects/finslertract

NeuroshareLibrary

This is MATLAB library to create Neuroshare data format.
You can convert your own data into Neuroshare format file.

Faceted Search Based Ontology Visualizer

Allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.

CBRAIN

CBRAIN is a flexible software platform with a small footprint and minimal requirements. CBRAIN was created to allow the integration the often extremely heterogeneous research HPC facilities across Canada and the World. Moreover, the platform's goal was not limited to deploying national and international distributed data and compute grids for neuroimaging sites, CBRAIN is an online collaborative web platform from which users transparently control their data, compute and results, including various forms of 2D and 3D data visualisation, regardless of where these resources and data are.

CBRAIN is currently deployed on 6 Compute Canada HPC clusters, one German HPC cluster and 3 clusters local to McGill University Campus, totaling more than 80,000 potential CPU cores.

Visit us at: http://cbrain.mcgill.ca

C8: Corpus Callosum Computations

C8 is a small, stand-alone MatLab toolbox that measures sagittal cross-section thickness and area of the human corpus callosum from high-resolution T1 in vivo MR images. C8 takes as input affine normalized white matter segmentations derived from high-resolution (in-plane) T1 images and outputs both regional callosal thicknesses in three different formats and geometrically-defined regional areas in three different configurations. It is a small package that is easily configurable and modifiable and it measures callosa at the rate of several per minute.

MABMIS: Multi-Atlas Based Segmentation

This software package implements MABMIS: Multi-Atlas-Based Multi-Image Segmentation – an algorithm for accurate and consistent segmentation/labeling on a group of images.

MR Connectome Automated Pipeline (MRCAP)

This is the project page for the MR Connectome Automated Pipeline based on JIST and MIPAV. The pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome, which is a comprehensive description of the wiring diagram of the brain.

Pydicom

pydicom is a pure python package for working with DICOM files. It was made for inspecting and modifying DICOM data in an easy "pythonic" way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements.

Lipsia

Lipsia is a software tool for processing functional magnetic resonance imaging (fMRI) data. It was developed over the course of several years at the Max-Planck-Institute for Human Cognitive and Brain Sciences in Leipzig, Germany.
Lipsia contains software tools for all aspects of fMRI data processing:

* registration and normalization
* preprocessing
* exploratory processing
* statistical evaluation
* region of interest analysis
* timecourse analysis
* visualization, rendering
* converters to various data formats

It was developed in C/C++ on Linux PCs. Lipsia provides extremely fast implementations. A standard analysis sequence from the raw data to a statistical parametric map generally takes less than 10 minutes per test subject.

MagPro Magnetic Stimulator (TMS)

MagPro is a complete line of non-invasive magnetic stimulation systems designed for clinical examinations and for research in the areas of neurophysiology, neurology, cognitive neuroscience, rehabilitation and psychiatry.

Convert MNI coordinates to or from XYZ

Input either normalized "MNI" coordinates from a 3D image, or input "real world" XYZ matrix coordinates, and this code will convert coordinates of one type to the other.

MriWatcher

This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time.
Very useful for quality control, image comparison.

Low Resolution Electromag TomogrAphy

LORETA (low resolution brain electromagnetic tomography) is a technique for functional imaging of the human brain. It computes the three dimensional distribution of electric neuronal activity (throughout cortical grey matter) from non-invasive measurements of scalp electric potential differences (EEG: electroencephalogram), with high time resolution in the millisecond range. The non-invasive intracranial time series are used for studying functional dynamic connectivity. The current software implementation is limited to EEG, although LORETA is defined for EEG and MEG (magnetoencephalogram). The standardized and exact versions of LORETA produce images with zero localization error.

GLIRT

GLIRT (Groupwise and Longitudinal Image Registration Toolbox) provides solutions for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications.

Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, we have included two of our recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short).

On the other hand, we also included our recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.

This software package was developed in the IDEA group at UNC-Chapel Hill ( http://bric.unc.edu/ideagroup ).

Open Connectome Project

The Open Connectome Project (OCP: openconnectomeproject.org) provides access to high resolution neuroanatomical images that can be used to explore connectomes. We also provide programmatic access to this data for human and machine annotation, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes.

Mouse Connectome Project (MCP)

The Mouse Connectome Project (MCP,http://www.mouseconnectome.org) aims to create a three-dimensional digital connectome atlas of the C57Black/6J mouse brain. MCP offers a catalog of neural tracer injection cases, which is updated continuously to eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome browser. Sample data set is available to explore in iConnectome. The data set features 5 layers which may be turned on, off, or adjusted for transparency, and split window features are available for comparing data sets.

The MCP project is housed at the Laboratory of Neuro Imaging at UCLA.

PPMI

PPMI includes a large and comprehensive set of correlated clinical data and biospecimens that is made available to the entire scientific community to help accelerate biomarker verification research. PPMI data and specimens have been collected in a standardized manner under strict protocols developed by the steering committee. The PPMI study dataset includes clinical, biological and imaging data collected at PPMI clinical sites. The data have been aggregated into the PPMI study database, which is managed by the PPMI Bioinformatics Core, the Laboratory of NeuroImaging (LONI) at the University of California, Los Angeles.

http://www.ppmi-info.org/access-data-specimens/

ADNI

Data collected as part of the ADNI study are freely available to authorized investigators, through the Image Data Archive (IDA). Information about obtaining access to ADNI data may be found in the How to Apply for Data section (http://adni.loni.ucla.edu/about-data-samples/).

For more detailed information about accessing data from the IDA, please review the IDA User Manual.

The following ADNI data types are available: Clinical: Demographics, Clinical Assessments, Cognitive Assessments); Imaging: MRI: Raw, pre- and post- processed image files; PET: Raw, pre- and post- processed image files; fMRI: (ADNI GO); DTI: (ADNI GO); Chemical Biomarker: Laboratory Results; Genetic: Illumina SNP genotyping; Image Analysis Results: Numeric results derived from image analyses.

The ADNI database is managed and housed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/) at UCLA.

Draw3D and Meshinator

Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK, it can render whatever VTK can render, and runs wherever VTK can run.

Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data.

Please see the wiki for documentation

INCF Neuroimaging Data Sharing

Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications.

The overall scope of this program is to develop generic standards and tools to facilitate the recording, sharing, and reporting of metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data.

BrainBrowser

BrainBrowser ( https://brainbrowser.cbrain.mcgill.ca ) is a web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface.

BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric.

In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data.

BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew

NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability.

CCSeg

Corpus Callosum Segmentation Tool

CCSeg is an open-source C++-based application developed at UNC-Chapel Hill that allows automatic as well as user-interactive segmentation of the Corpus Callosum. Via a Qt-based graphical user interface, CCSeg also performs semi-automatic segmentation.

NIRAL Utilities

NIRAL Utilities are open-source applications developped at UNC-Chapel Hill in the Neuro Image Research and Analysis Lab (NIRAL). These utilities are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries.

Finsler tractography module for Slicer

This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost.

The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required).

The software can be built as either a stand-alone or a CLI plugin for 3D Slicer.

Bisque

Bisque (Bio-Image Semantic Query User Environment) is a scalable web-based system for biological image analysis, management and exploration. The Bisque system incorporates many features useful to imaging researchers from image capture to extensible image analysis and querying. At the core, bisque maintains a flexible database of images and experimental metadata. Image analyses can be incorporated into the system and deployed on clusters and desktops.

MASI Label Fusion

This collection of tools is maintained by the Medical-image Analysis and Statistical Interpretation (MASI) group at Vanderbilt University.

The purpose of this tool is to provide a unified framework for testing and applying statistical and voting label fusion techniques. The project will include implementations of several different voting techniques including majority vote, weighted voting, and regionally weighted voting. Additionally, multiple statistical fusion methods will be included, notably, STAPLE, Spatial STAPLE, STAPLER and COLLATE.

In addition to the fusion algorithms, code for running specialized simulations and various tools and utilities to test the efficacy of the algorithms will be provided.

fMRI Classification in R

We demonstrate and provide R code that can classify between groups of fMRI scans based on functional network connectivity differences, requiring only 4 lines of code to be altered. In addition, we include a detailed article explaining the methods behind and motivations of this tool. This code can also be altered to perform connectivity analysis and classification using ROI based methods by reading in distance arrays previously created. We run ICA on fMRI data to establish functional networks, measure the functional connectivity between these networks using the temporal cross-correlations between independent component to create a distance matrix and indicating the networking. Connectivity properties are used as a feature matrix for an SVM classifier. Collectively, this project provides and explains both methods and code to perform functional network connectivity and fMRI SVM classiﬁcation.

Paradigm

Flexible and millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Build your experiments using Paradigm's simple drag and drop interface. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available to ensure total flexibility and control. Joystick and microphone response are available. Supports button boxes from PST, Cedrus and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs.

Cluster reporter

This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons, but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases (borrowed from other software) to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition, it will output statistics for each surviving cluster, and the image as a whole.Feedback would be much appreciated.

Cluster Extent Correction

This script will take any .img file and correct it based on a cluster extent, cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately, and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox.

A Generalized Form of PPI

An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST.

The automated toolbox can do the following:
(a1) produce identical results to the current implementation in SPM
(a2) use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate
(a3) uses a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate
(b) creates the model using the output of one of the (a) options and the first level design
(c) estimates the model (/results directory)
(d) computes the contrasts specified

HCP WU-Minn Consortium

*THE HUMAN CONNECTOME PROJECT WU-Minn Consortium* The Consortium will acquire and analyze several modalities of neuroimaging data plus behavioral and genetic data from 1200 healthy adults (300 twin pairs and siblings). The project will yield invaluable information about brain connectivity, its relationship to behavior, and contributions of genetic and environmental factors to individual differences in brain circuitry. Data will be shared with the scientific community via a user-friendly platform for data mining, analysis, and visualization. Phase I involves optimization of data acquisition and analysis methods. Phase II (2012-2015) will involve data acquisition from 400 subjects/year. The Consortium includes investigators at 10 institutions, co-lead institutions Washington U. and the U. of Minnesota, Oxford U., St. Louis U., Advanced MRI Technologies with UC Berkeley, Indiana U., the U. G. d’Annunzio, Radboud U. Nijmegen, the Ernst Strüngmann Institute, and Warwick U. www.humanconnectome.org

Connectome File Format (CFF)

The Connectome File Format (CFF) is a container format for multi-modal neuroimaging data. It comprises connectome objects of type: CMetadata, CNetwork, CVolume, CSurface, CTrack, CScript, CData, CTimeseries, CImagestack. The Python library cfflib provides read/write functionality.

CIFTI Connectivity File Format

CIFTI (Connectivity Informatics Technology Initiative) standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties.

Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats.

Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email.

pyxnat

pyxnat is a simple python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

COMPARE

COMPARE :Generic classification tool for 3D images

BRAINSImageEval

BRAINSImageEval is a Qt-based GUI application designed for radiologists and trained raters to quickly evaluate MRI and other 3D medical images.

MRI Dataset for Hippocampus Segmentation

This dataset contains T1-weighted MR images of 50 subjects, 40 of whom are patients with temporal lobe epilepsy and 10 are nonepileptic subjects. Hippocampus labels are provided for 25 subjects for training. The users may submit their segmentation outcomes for the remaining 25 testing images to get a table of segmentation metrics. More information about the dataset may be found from the following reference:

K. Jafari-Khouzani, K. Elisevich, S. Patel, and H. Soltanian-Zadeh, “Dataset of magnetic resonance images of nonepileptic subjects and temporal lobe epilepsy patients for validation of hippocampal segmentation techniques,” Neuroinformatics, 2011.

MeshValmet: Validation Metric for Meshes

MeshValmet is a tool that measures surface to surface distance between two triangle meshes using user-specied uniform sampling. Thus, users can choose finer sampling level to calculate errors to gain more accuracy in the "error space", or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries.

Besides its pleasant visualization using the VTK library, MeshValmet also provides useful histogram and statistical information based on the sample errors, such as mean and median distance, root mean square distance, mean square distance, mean absolute distance, Hausdor distance, 95 percentile, 68 percentile, etc.

MeshValmet is based on the work of Nicolas Aspert, etc.: MESH: Measuring Errors between Surfaces using the Hausdor distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 (ICME), vol. I, pp. 705-708.

The calculation of the Dice's Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum.

TurtleSeg

TurtleSeg is an interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process.

fanDTasia Java Applet: DT-MRI Processing

FanDTasia is a Java applet tool for DT-MRI processing. It opens dw-mri datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

HAMMER Suite

The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration.

I/OWA 3

I/OWA 3: Input / Output time aWare Architecture

AHEAD

Automatic Hippocampal Estimator using Atlas-based Delineation (AHEAD) is an open-source turnkey software for automatic hippocampus segmentation. Its primary use is for delineating hippocampus in T1-weighted MRI images. AHEAD is developed by Jung W. Suh, Hongzhi Wang, Sandhitsu Das, Brian Avants, Philip Cook, John Pluta and Paul Yushkevich, and colleagues at the Penn Image Computing and Science Laboratory (PICSL) at the University of Pennsylvania.

Functional Regression Analysis of DTI

Functional Regression Analysis of DTI Tract Statistics (FRATS), for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.

Functional Analysis of Diffusion Tensor

A functional analysis of diffusion tensor tract statistics (FADTTS) pipeline was developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands.

ShapeWorks

The ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

DOTS

Diffusion-Oirented Tract Segmentation (DOTS) is a fast, scalable tool developed at the Johns Hopkins University to automatically segment the major anatomical fiber tracts within the human brain from clinical quality diffusion tensor MR imaging. With an atlas-based Markov Random Field representation, DOTS directly estimates the tract probabilities, bypassing tractography and associated issues. Overlapping and crossing fibers are modeled and DOTS can also handle white matter lesions.

DOTS is released as a plug-in for the MIPAV software package and as a module for the JIST pipeline environment. They are therefore cross-platform and compatible with a wide variety of file formats.

RFT_FDR

So far there is a lack for Random Field Theory(RFT)-based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley’s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer’s matlab subdirectory in the Matlab’s search path.

In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).

WhiteText - annotated neuroscience text

WhiteText is a corpus of manually annotated brain region mentions. It was created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 17,585 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words.

The corpus can be found at http://www.chibi.ubc.ca/WhiteText/

Previous evaluation of automated recognition of the mentions is described in:
"Automated Recognition of Brain Region Mentions in Neuroscience Literature"
by French, Lane, Xu and Pavlidis.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741206/

NIREP

We have started the Non-rigid Image Registration Evaluation Project (NIREP) to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria.

The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.

Scalable Brain Atlas

The INCF Scalable Brain Atlas (scalablebrainatlas.incf.org) is a web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy.

Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required).

The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations.

Robust Biological Parametric Mapping

Biological parametric mapping has extended the widely popular statistical parametric approach to enable application of the general linear model to multiple image modalities (both for regressors and regressands) along with scalar valued observations. This approach offers great promise for direct, voxelwise assessment of structural and functional relationships with multiple imaging modalities. However, as presented, the biological parametric mapping approach is not robust to outliers and may lead to invalid inferences (e.g., artifactual low p-values) due to slight mis-registration or variation in anatomy between subjects. To enable widespread application of this approach, we introduce robust regression and non-parametric regression in the neuroimaging context of application of the general linear model.

IIT2 DTI Human Brain Template

The IIT2 diffusion tensor template of the human brain was developed using artifact-free Turboprop-DTI data collected on 67 subjects. The template is in ICBM-152 space, allowing use of ICBM resources.
Advantages of the IIT2 template: a) constructed based on a large number of subjects with a limited age-range, b) no artifacts, c) even small white matter structures are visible, d) high image sharpness, e) low noise levels, f) DTI information that is representative of single-subject data, g) excellent matching to ICBM-152 space.
The following information is provided in NIfTI format and 1mm isotropic resolution: Mean DW and b=0 maps. Mean and median tensors. FA, trace, eigenvalues, eigenvectors of mean and median tensors. Standard deviation of mean and median FA and trace, cone of uncertainty and total variance of mean and median tensors.
When using the IIT2 template please cite: Zhang S, Peng H, Dawe RJ, Arfanakis K. Enhanced ICBM diffusion tensor template of the human brain. Neuroimage 2011;54:974–984.

resting-state pediatric imaging template

Group ICA was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. We have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

MouseTracker

MouseTracker is a free, user-friendly software package that allows researchers to record and analyze real-time hand movements en route to responses on the screen (via the coordinates of an MR-safe mouse, trackball, or sensor). By looking at how the hand settles into a response alternative--and how it may be partially pulled toward other alternatives--researchers glean information about real-time mental processing. It's like opening up a single reaction time into a continuous stream of rich cognitive output. Experiments can incorporate images, letter strings, and sounds. Once recorded, participants' mouse trajectories can be visualized, averaged, and explored, and measures of curvature, complexity, velocity, acceleration, and angle can be computed. Precise characterizations of mouse trajectories' temporal and spatial dynamics are available, and these can shed light on a variety of important empirical questions across psychology, neuroscience, and beyond.

DTI-TEMPLATE-RHESUS-MACAQUES

Diffusion Tensor Imaging (DTI) studies of non-human primates (NHP) are becoming increasingly common. Recently, many DTI analysis methodologies have been developed for human brain studies; however, few are directly applicable to NHP. A prerequisite for most statistical DTI analyses to localize WM differences across populations is to spatially normalize the individual scans to a representative template. Here, we report the development of a population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Our DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that our DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.

NeuroPub Visualizer

NeuroPub is a NIfTI visualisation tool for the iPad. You can use it to store all your statistical images from your fMRI/VBM/TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. You can download the app for free from the App Store!

Spatially Constrained Parcellation

Source code and parcellations now available! Go to MediaWiki on the left for more information.

Spatially constrained parcellation is a set of tools for deriving ROI atlases by whole brain clustering of task or resting state data. In addition to the tools, this resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al., A whole brain fMRI atlas generated via spatially constrained spectral clustering, which is currently in revision in Human Brain Mapping.

The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python, numpy and scipy to run.

IMOD - 3D Reconstruction and Analysis

IMOD is a free, cross - platform set of image processing, modeling and display programs used for tomographic reconstruction, reconstruction and segmentation of 3D volumes. IMOD has tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3D data from any orientation, and modeling and displaying the image files.

Tractography with Unscented Kalman Filte

We present a framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model.

It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation.

The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application.

Web Interfaces for Multiscale Images

This is a venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions.

Please visit our Wiki to start participating.

Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web.

AutoSeg

AutoSeg is a novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation.

AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data.

AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes.

BRAINSSurfaceStats

This program provides a tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

Viking Viewer for Connectomics

Viking is a multi-user modular viewing and annotation system which functions with any type of stacked 2D imagery. Originally designed for transmission electron microscopy connectome data Viking has been used for confocal, bright field, and OCT images. Available from:

http://connectomes.utah.edu/

A paper describing Viking is here:
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2010.03402.x/abstract

Viking requires images be available over HTTP and follow a standard URL naming convention with basic meta-data in an accompanying XML file. Consult the website or author about making images/volumes compatible with Viking. Viking is capable of texture mapping images in real-time on to meshes using the GPU if needed. Viking runs on Windows.

An optional annotation module allows concurrent markup of data sets via a WSDL web service and requires a separate server installation. Server installation is non-trivial and until it improves we are open to hosting databases on the our annotation server.

HCP Harvard/MGH-UCLA

***THE HUMAN CONNECTOME PROJECT Harvard/MGH-UCLA***

The HCP is a multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and UCLA; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization.

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

See http://www.humanconnectomeproject.org or http://www.humanconnectome.org for details.

Disease State Prediction

These are the scripts used for the analyses reported in: Craddock RC, Holtzheimer PE, 3rd, Hu XP, Mayberg HS. (2009): Disease state prediction from resting state functional connectivity. Magn Reson Med 62(6):1619-28.

Specifically included are scripts for performing t-test filter, reliability filter, recursive feature elimination, and reliability recursive feature elimination feature selection methods. These make use of wrappers that perform .632 bootstrap and k-fold cross validation strategies. The scripts are written in matlab and require the Bioinformatics toolbox. If you do not have the bioinformatics toolbox, the scripts can be easily modified to run with other matlab SVM toolboxes (i.e., libsvm, svmlight, shogun, etc.).

SPM_SS - fMRI functional localizers

This spm-toolbox performs ROI-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers.

Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics)

This toolbox requires Matlab and SPM5/SPM8.

http://web.mit.edu/evelina9/www/funcloc.html

vuTools

This site provides access to the VUIIS Image and Data Analysis Core's data processing tools written for MATLAB. These tools are written for ease of use from within MATLAB. Unless stated otherwise, each of the tools is capable of processing 2D/3D images (matrices).

ANTsR

ANTsR is an R extension to ANTs that performs multivariate statistical parametric mapping of DTI, T1 and other datatypes for the purpose of both performing clinical studies and for tracking the performance of ANTs (and other) image processing methodologies. ANTsR depends upon the R statistical language, bash scripts and the ANTs toolkit. Some branches of ANTsR will also depend upon pipedream and specific datasets. Some of these datasets will be open access and, in that case, ANTsR will provide a 100% reproducible neuroimaging study on that data.

NeuroImaging Analysis Kit (NIAK)

NIAK is a library of modules and pipelines for fMRI processing with Octave or Matlab(r) that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a T1 preprocessing pipeline, a pipeline for correction of structured noise by component selection in ICA (CORSICA), as well as an fMRI preprocessing pipeline. NIAK features powerful pipeline management capabilities, including parallel computing, generation of detailed logs and automatic handling of pipeline failures or updates.

GIMIAS

GIMIAS is a workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology.

Distributome

The Distributome Project is an open-source, open content-development project for exploring, discovering, navigating, learning, and computational utilization of diverse probability distributions.

TetraMetrix

TetraMetrix is an open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. The project is being developed by researchers at UCLA Laboratory of Neuro Imaging (http://www.LONI.ucla.edu) and Department of Mathematics (http://www.math.ucla.edu).

A beta version of the program is available for download. Please see the very brief instructions on the 'Docs' tab on the left.

TetraMetrix is distributed by the Laboratory of Neuro Imaging at UCLA.

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: Large Data Set ANOVA

CLEAVE is a UNIX-style command-line program which quickly computes multifactorial ANOVAs for very large 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: port CLEAVE-style data sets in or out of MATLAB.

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 package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions.

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.

NITRC GForge Extensions

This project contains custom extensions to the GForge collaborative environment used to create NITRC. These features include: MediaWiki integration, ratings and reviews, Nutch Web crawling integration, improved project searching, BBCode extensions, and front and project summary page re-design. See our Release Notes page for specifics: http://www.nitrc.org/plugins/mwiki/index.php/nitrc:NITRC_Release_Notes

Vervet Probabilistic Atlas

The vervet (Chlorocebus aethiops sabaeus) 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.

MASIMatlab

The MASI research laboratory concentrates on analyzing large-scale cross-sectional and longitudinal neuroimaging data. Specifically, we are interested in population characterization with magnetic resonance imaging (MRI), multi-parametric studies (DTI, sMRI, qMRI), and shape modeling.

This repository stores and provides opportunities for collaboration through Matlab code, libraries, and configuration information for projects in early stage development.

GAMBIT

GAMBIT is an end-to-end application developped at UNC-Chapel Hill allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line.

The Neuro Bureau

The Neuro Bureau is neuro-collaboration in action.

More specifically the Neuro Bureau is a neuroscience collaboratory that supports open neuroscience. To join the Neuro Bureau use the "join the team" link in the yellow box to the right. For more information, please contact: theneurobureau@gmail.com

Preprocessed imaging data can be downloaded using the Downloads link on the left, for more information on the preprocessed data use the MediaWiki link on the left.

Brain-Art Competition 2011 is now over. All of the submissions and the winners are posted at the Brain-Art Gallery.
neurobureau.projects.nitrc.org/BrainArt/Gallery

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.

Vaa3D and Vaa3D-Neuron

Vaa3D (3D Visualization-Assisted Analysis) is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D 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.

Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins.

Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-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 (fMRIDC). 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.

PNVE is distributed by the Laboratory of Neuro Imaging (http://pipeline.loni.ucla.edu/PNVE) at UCLA.

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 v4.5.

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 4.5.

ImageVis3D

Note ImageVis3D development is hosted elsewhere -- see http://www.imagevis3d.org/

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.

Connectome Viewer

Connectome Viewer 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 software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped 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

The pipeline system for Octave and Matlab (PSOM) is a lightweight library to manage complex multi-stage data processing. A pipeline is a collection of jobs, i.e. Matlab or Octave codes with a well identified set of options that are using files for inputs and outputs. To use PSOM, the only requirement is to generate a description of a pipeline in the form of a simple Matlab/Octave structure. PSOM then automatically offers the following services:

* Run jobs in parallel using multiple CPUs or within a distributed computing environment.
* Generate log files and keep track of the pipeline execution. These logs are detailed enough to fully reproduce the analysis.
* 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 !

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.

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”, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047

DTIProcess ToolKit

DTIProcess 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

Download jip-overview.pdf to see if these tools interest you.
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, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 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 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.

ShapeViewer is distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/ShapeViewer) at UCLA.

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.

Provenance Editor is distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/ProvenanceEditor) at UCLA.

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.

FFT toolbox is distributed by the Laboratory of Neuro Imaging (http://www.loni.ucla.edu/Software/FFT) at UCLA.

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.

SHIVA is distributed by the Laboratory of Neuro Imaging (http://www.loni.ucla.edu/Software/SHIVA) at UCLA.

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.

MultiTracer is distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/MultiTracer) at UCLA.

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.

AIR is distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/AIR) at UCLA.

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.

Brain Parser is distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/BrainParser) at UCLA.

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.

ShapeTools are distributed by the Laboratory of Neuro Imaging (http://www.LONI.ucla.edu/Software/ShapeTools) at UCLA.

Center for Computational Biology (CCB)

The Center for Computational Biology (http://www.CCB.ucla.edu) provides 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data).

CCB is headquartered at the Laboratory of Neuro Imaging (http://CCB.LONI.ucla.edu/) at UCLA.

ABC (Atlas Based Classification)

ABC (Atlas Based Classification) is a comprehensive processing pipeline developed and used at University of North Carolina and University of Utah for brain MRIs. The processing pipeline includes image registration, filtering, segmentation and inhomogeneity correction. The tool is cross-platform and can be run within 3D Slicer or as a stand-alone program.

The image segmentation algorithm is based on the EMS software developed by Koen van Leemput.

1000 Functional Connectomes Project

ATTENTION: The 1000 Functional Connectomes Project has a new home page at NITRC. Please visit us at:
http://fcon_1000.projects.nitrc.org or simply click on 'DOWNLOAD NOW' below to be redirected.

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

Human brain atlases have been generated at UNC-Chapel Hill for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures.

Current available atlases:
- Adult atlas:
Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old).
- UNC-MNI Pediatric 1-year-old atlas:
Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls.
- Pediatric 4-year-old atlas:
Symmetric atlas generated from 10 4-year-old healthy subjects.
- Elderly atlas:
Atlas generated from 27 healthy elderly subjects (60+ years old).

Additional information and acknowledgment for their usage can be found by clicking on the release notes.

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 NIH Human Connectome Project is an effort to map the neural pathways that underlie human brain function. The purpose of the Project is to acquire and share data about the structural and functional connectivity of the human brain. It will advance the capabilities for imaging and analyzing brain connections, resulting in improved sensitivity, resolution, and utility.

The NIH Blueprint for Neuroscience (http://www.neuroscienceblueprint.nih.gov/) has funded two grants that will take complementary approaches:

* A consortium led by Washington University in St. Louis and the University of Minnesota will enable development and utilization of advanced MRI methods to chart brain circuitry. http://www.humanconnectome.org/

* A consortium led by Massachusetts General Hospital and the University of California at Los Angeles will enable building a next-generation 3T MR scanner that improves the quality and spatial resolution of brain connectivity data. http://www.humanconnectomeproject.org/

CONN - fMRI functional connectivity

Toolbox for functional connectivity analyses of fMRI data

* Seed-to-voxel analyses: Analyze the connectivity between one or multiple seed areas and the whole brain
* ROI-to-ROI analyses: Analyze the connectivity between multiple ROIs, as well as graph-theoretical properties of the resulting networks
* Voxel-to-voxel analyses: Analyze the whole-brain connectome without using a priori seeds/ROIs

Available for resting state data as well as task-related block designs. Gui and automated batch processing

Method highlights: Complete spatial preprocessing pipeline; CompCor method for removing physiological and movement confounds; Multiple seed-to-voxel and ROI-to-ROI linear connectivity measures; Whole-brain multivariate pattern analyses of connectivity maps, and estimation of several descriptive connectivity indexes; Univariate and multivariate group-level analyses (mixed within- between-subjects designs)

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).

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

NOTE: All new development is being managed in a github repository. Please visit

https://github.com/BRAINSia/BRAINSStandAlone

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

NOTE: All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to

https://github.com/BRAINSia/BRAINSStandAlone

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-SA 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

Free article on PMC: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788

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; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model).

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

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-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 0-1-2 Infant Atlases

Keyword: Infant; Pediatric; Template; Atlas; Longitudinal
There are 3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

Please refer to the following article for the atlases:
Feng Shi, Pew-Thian Yap, Guorong Wu, Hongjun Jia, John H. Gilmore, Weili Lin, Dinggang Shen,"Infant Brain Atlases from Neonates to 1- and 2-year-olds", PLoS ONE, 6(4): e18746, 2011.

For more information and download link, please visit:
http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases

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).

DicomBrowser

DicomBrowser 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. DicomBrowser includes scriptable header editing to support various de-identification protocols. Dicomrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation. For more information: http://nrg.wustl.edu/software/dicom-browser

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 an 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 elastic registration algorithm for medical images, matching morphological signatures of images in a hierarchical multi-scale regime.

White matter lesion (WML) segmentation is a novel multi-spectral WML segmentation protocol via incorporating information from T1-w, T2-w, PD-w and FLAIR MR brain images. (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 regional 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

NOTE: All active development of BRAINSMush is now being stored in a Git repository at github.com. Please go to

https://github.com/BRAINSia/BRAINSStandAlone

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 INCF is a professional organization devoted to advancing the field of neuroinformatics. One of its aims is to develop an international neuroinformatics infrastructure, which promotes the sharing of data and computing resources to the international research community. A second objective of INCF is to help develop scalable, portable, and extensible applications that can be used by neuroscience laboratories worldwide.

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

NOTE: All new development is being managed in a github repository. Please visit

https://github.com/BRAINSia/BRAINSStandAlone

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.

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

NOTE: All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to

https://github.com/BRAINSia/BRAINSStandAlone

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 ).

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 support of information about upcoming Conferences, Workshops and Meetings. Such support may be documents, news, files, etc.

To see a listing of upcoming Events, please use the NITRC Community Events Page at http://www.nitrc.org/incf/event_list.php (and tab at right).

To announce an Event, please use the "Submit an Event" at the NITRC Community Events Page, http://www.incf.org/Events/events/createObject?type_name=Event (and tab at right). Note, INCF account is currently required.

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).

iTools is distributed by the Laboratory of Neuro Imaging (http://www.loni.ucla.edu/Software/iTools) at UCLA

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. SPM8).

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

XCEDE Schema

XML-Based Clinical Experiment Data Exchange Schema (XCEDE)provides an extensive metadata hierarchy for describing and documenting research and clinical studies.

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. More information can be found at http://www.nitrc.org/projects/nutmeg/

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 Download link on this page. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

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. It's emphasis is on enabling the sharing of biomedical data through a suite of software capabilities. It currently consists of expertise in Data Movement, Data Security, Mediation Across Data Sources, Knowledge Engineering, Workflows, and Genetics. The main BIRN site is at the Information Sciences Institute at USC with collborators at the University of Chicago, the Massachusetts General Hospital, University of California, Irvine and University of California, Los Angeles.

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 viewer for medical research images. It provides analysis tools and a user interface to navigate image volumes. There are three versions of Mango, each geared for a different platform:

* Mango – Desktop – Mac OS X, Windows, and Linux
* webMango – Browser – Safari, Firefox, Chrome, and Internet Explorer
* iMango – Mobile – Apple iPad

Key Features:
- Built-in support for DICOM, NIFTI, Analyze, and NEMA-DES formats
- Customizable: Create plugins, custom filters, color tables, file formats, and atlases
- ROI Editing: Threshold and component-based tools for painting and tracing ROIs
- Surface Rendering: Interactive surface models supporting cut planes and overlays
- Image Registration: Semi-automatic image coregistration and manual 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

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 analysis of Magnetic Resonance Spectroscopy (MRS) data by registering it to anatomical images. BrainCSI imports LCModel results to calculate absolute metabolite concentrations using tissue water. Corrections to LCModel metabolite concentrations for partial volume of tissues are accomplished by tissue classification of the anatomical images.

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

ART `acpcdetect' program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans.

ART `brainwash' program for automatic multi-atlas skull-stripping of 3D structural MRI scans.

ART `3dwarper' program of non-linear inter-subject registration of 3D structural MRI scans.

Software (art2) for linear rigid-body intra-subject inter-modality (MRI-PET) image registration.

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

NOTE: All new development is being managed in a github repository. Please visit

https://github.com/BRAINSia/BRAINSStandAlone

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. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains. The new BIRN incarnation can be found at http://www.birncommunity.org

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

NOTE: All active development of BRAINSConstellationDetector is now being stored in a Git repository at github.com. Please go to

https://github.com/BRAINSia/BRAINSStandAlone

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. Note: the code here was part of a doctoral dissertation from 2005, is written in Matlab and has FSL 3.2 as a dependency. A new version is under development and will be completed in 2012. 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. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Visit http://pipeline.loni.ucla.edu for more info.

The Pipeline is distributed by the Laboratory of Neuro Imaging (http://www.loni.ucla.edu/Software/Pipeline) at UCLA.

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.