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IVAN runs the Ubuntu Desktop Edition 10.04 LTS 64 bit platform. All standard Linux packages are included. In addition, we have installed the following packages to create an integrated neuroimaging analysis environment. This operating system and application software platform is also available as the IBIC "Evolution" Virtual Machine, which can be run on other platforms (e.g., PC, Mac).

Neuroimaging Software

Description

For More Information

afni (latest from NeuroDebian)

Analysis of Functional Neuroimages: A set of programs for processing, analyzing, and displaying functional MRI (FMRI) data

link

ANTS (Advanced Normalization Tools) 1.9.1

The ANTS framework provides open-source functionality for deformable normalization with large deformations. Small deformation mappings and segmentation tools are also available.

link

AIR 5.2.6

AIR allows automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities.

link

ART

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

link

artfind

Read motion parameters from an FSL, BrainVoyager, or AFNI parameter file, find points where the absolute or relative motion exceeds settable threshold values, and generate a set of single point artifact regressors to model out these points. Based on the interactive tool "ART" by Susan Whitfield-Gabrieli

 

bioimagesuite

BioImage Suite is an integrated image analysis software suite developed at Yale University. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be integrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

link

Brains3 (Alpha)

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.

link

Brainvox 3.14

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).

link

camino

Camino is a software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.

link

camino-trackvis

This package allows interoperability between CAMINO and TRACKVIS

link

dicom3tools

DICOM and other image format conversion and manipulation tools

see Manual pages, link

Diffusion Toolkit (DTK)

Diffusion Toolkit is a set of command-line tools with a GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. Basically, it does the preparation work for TrackVis.

link

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.

link

fMRIstat

A general statistical analysis for fMRI data.

link

Freesurfer (4.5 and 5.0)

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.

IBIC instructions, link

FSL 4.1.6

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

link

GroupICA Toolbox (GIFT 1.3)

GIFT is a MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data.

link

MRIConvert

MRIConvert is a medical image file conversion utility that converts DICOM files to NIfTI 1.1, Analyze 7.5 , SPM99/Analyze, BrainVoyager, and MetaImage volume formats.

link

mricron (latest from NeuroDebian)

NIFTI viewer and dcm2nii DICOM conversion

link

mtrix 0.2.9

MRtrix provides a set of tools to perform diffusion-weighted MRI white matter tractography in the presence of crossing fibres, using Constrained Spherical Deconvolution (Tournier et al.. 2004; Tournier et al. 2007), and a probabilisitic streamlines algorithm (e.g. Behrens et al., 2003; Parker et al., 2003).

link

nipy

Neuroimaging in Python tools

link

pymvpa

Multivariate pattern analysis in Python. 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.

link

Princeton MVPA toolbox (for MATLAB)

The MVPA Toolbox is a set of Matlab tools to facilitate multi-voxel pattern analysis of fMRI neuroimaging data.

link

pydicom

Read, write, manipulate DICOM files with Python code.

link

psychopy

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.

link

REST

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

link

SPM 8

Statistical Parametric Mapping (SPM) refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.

link
Tutorials

tal_tools

Brainvox tal_programs. Command line orientated tools which are scripted together to perform volume imaging tasks. Designed for use in MRI and PET neuroimaging

See manual pages

trackvis

TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography.

link

TractoR 1.7.0

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.

link

VBM 8

The VBM8 toolboxes are a collection of extensions to the segmentation algorithm of SPM8 (Wellcome Department of Cognitive Neurology) to provide voxel-based morphometry (VBM).

link
Tutorials

xmedcon

An open source toolkit for medical image conversion

link


Language Tools and Compilers

Description

For More Information

Cmake 2.8.3

CMake is a cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice.

link

gcc, g++ (latest version)

GNU C, C++ compilers and development environment

link

gfortran 4.4.3

GNU Fortran compiler

link

Google Data (Python) Library

Python interfaces for reading, writing, and modifying information on the web in google documents and spreadsheets.

link

Insight Toolkit (ITK) 3.20.0

ITK is an open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis. ITK employs leading-edge algorithms for registering and segmenting multidimensional data.

link

java SE 6 JDK

JAVA Programming language development kit

link

emacs 2.3

GNU Emacs text editor

link

nibabel

Python-based read and write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2), GIFTI, NIfTI1, MINC, as well as PAR/REC. NiBabel is the successor of PyNIfTI.

link

| STAT (Pipe Stat)

A small set of command-line statistics and data analysis programs

see Manual pages

python (Enthought distribution 6.3-1)

A comprehensive set of Python language tools to perform rigorous data analysis and visualization.

link

python profiler 2.6.5

This profiler provides deterministic profiling of any Python programs. It also provides a series of report generation tools to allow users to rapidly examine the results of a profile operation.

link

line profiler 1.0b2

line_profiler will profile the time individual lines of code take to execute. The profiler is implemented in C via Cython in order to reduce the overhead of profiling.

link

MATLAB R2010b

MATLAB® is a high-level language and interactive environment. Toolboxes included: Statistics, Neural Network, Fuzzy Logic, Signal Processing, Image Processing, Optimization and Parallel Computing

link

nipype

Python-based workflows and interfaces for neuroimaging

link

ppss

PPSS is a Bash shell script that executes commands, scripts or programs in parallel. It is designed to make full use of current multi-core CPUs. It will detect the number of available CPUs and start a separate job for each CPU core. It will also use hyper threading by default.

link

Octave 3.2

GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. The Octave language is quite similar to Matlab so that most programs are easily portable.

link

R (latest version)

A free software environment for statistical computing and graphics.

link

rpy2

Simple access to R from python, including wrappers to graphical libraries and R-like structures and functions.

link

SQL Lite

SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.

link

Visualization Toolkit (VTK) 5.6.1

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

link


Graphing and Visualization

Description

For More Information

geomview (latest version)

Interactive 3-D viewing program

link

gnuplot 4.0

Portable command line graphing utility

link


Other Utilities

Description

For More Information

audacity

Audacity is free, open source software for recording and editing sounds.

link

Chrome

The popular and fast Google Chrome browser.

link

Dropbox

Dropbox allows you to sync your files online and across your computers automatically.

link

NXClient

NXClient and FreeNX server allow you to connect to IVAN from your computer with remote-desktop like functionality.

IBIC Instructions, link

Oracle Virtual Box 4.0

VirtualBox is a powerful x86 and AMD64/Intel64 virtualization product that allows you to create and run virtual machines.

link

Oracle Grid Engine 6.2 Update 6

 

link

recode

Convert files between various character sets and usages.

link

sox

SoX is a cross-platform (Windows, Linux, MacOS X, etc.) command line utility that can convert various formats of computer audio files in to other formats. It can also apply various effects to these sound files, and, as an added bonus, SoX can play and record audio files on most platforms.

link

truecrypt

Disk encrpytion software

link

wine 1.2

Wine lets you run Windows software on other operating systems. With Wine, you can install and run these applications just like you would in Windows.

link

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