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Starting 2020.04.10, IBIC computers runs the Debian 10.3 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

Version

Description

For More Information

afni

20.

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

2.3.2

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

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

latest from NeuroDebian

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

5.3

6.0

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

5.0.9

6.0.3

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

mrtrix

0.2.12

3.0

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

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

SPM

8, 12

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

System Libraries:

Language Tools and Compilers

Version

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 11 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

Anaconda3 (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

MATLAB

R2019a

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

4.4

from Debian system

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

3.6

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

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 (2014 1.9)

Interactive 3-D viewing program

link

gnuplot 4.0

Portable command line graphing utility

link

Other Utilities

Version

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

6.1

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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