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Software in the N4U Environment for Neuroscientific Communities

 

 

 

 

N4U offers a range off applications and the computational resources to run them to several neuroscience research communities including neurodegenerative (NS-NDD), white matter (NS-WMD) and psychiatric diseases (NS-PSY).

 

The applications receiving most of our time and attention are primarily the ones most requested by the users. We also make available novel applications in neuroscience research developed by smaller groups.   

 

In the table below you will find a list of software either currently available on neuGRID or planned for future release. The list will be updated based on request from users, the practicalities of implementing the software and related issues.  

 

Several of the tools listed are already available on neuGRID (click here) through ExpressLane, a custom interface designed for running medical research applications under high performance computing on large numbers of scans.

 

 

Software

Community

Clinical/Biological Phenomenon of study

DESCRIPTION

  Resources Required

Status

FREESURFER

NS-NDD

NS-WMD

Study of cortical and subcortical anatomy

FreeSurfer is a set of automated tools for reconstruction of the brain's cortical surface and other brain structures from MRI data. A few key applications have been implemented as official scripts in ExpressLane, which as well as providing useful applications, also provide examples of how to implement many other FreeSurfer applications.

 Available

FREESURFER ReconAll Cross Sectional

NS-NDD

NS-WMD

 Study of cortical and subcortical anatomy For a single MRI scan, segments cortical and subcortical anatomy - including the hippocampus - and calculate areas and thickness. 2GB, 1 day, single core

FREESURFER ReconAll Longitudinal

NS-NDD

NS-WMD

 Study of cortical and subcortical anatomy For a pair of MRI scans, segments cortical and subcortical anatomy - including the hippocampus - and calculate areas, thickness and change in volumes 2GB, 3 to 5 days, single core

FREESURFER Tracula

NS-NDD

NS-WMD

NS-PSY

 Study of tractographic (DTI) anatomy of the brain A tool for automatic reconstruction of a set of major white-matter pathways from diffusion-weighted MR images 2GB, 1 to 2 days, single core

MAPS-HBSI

.

NS-NDD

NS-WMD

NS-PSY

Hippocampal and whole brain volume change over time - atrophy measures. Preliminary results show MAPS-HBSI to be 50% more reproducible than the standard in the field - FreeSurfer/ReconAll and manual. AAIC2014 Poster Neuroimage. 2010 Jul 15;51(4):1345-59.

 

 Newly implemented algorithm. Restricted access - contact N4U. 4GB, 3 to 5 days, single core

FSL

NS-NDD

NS-WMD

NS-PSY

Study of functional (fMRI), structural (MRI) and  tractographic (DTI) anatomy of the brain

A library of image analysis for MRI, functional MRI and diffusion tensor imaging brain imaging data. A few key applications have been implemented as official scripts in ExpressLane, which as well as providing useful applications, also provide examples of how to implement many other FSL applications.

 Available

FSL TBSS - N2

NS-NDD

NS-WMD

NS-PSY

 Track Based Spatial Statistic - Find the "typical" image volume among a set for factional anisotropy (FA).

Superior version of the widely used algorithm. neuGRID's multicore implementation reduces computation time by factor of 24 making the rarely used but superior N2 implementation of TBSS practical.

 N2 time,  144 scans takes about 6 days, multicore

FSL FIRST

NS-NDD

NS-WMD

 Study of  structural (MRI) Widely used FSL algorithm that segments the left and right hippocampi from MRI scans. Takes 20 to 30 minutes per scan. 2GB, under 1 hour, single core

FSL SIENA

NS-NDD

NS-WMD

 Study of structural (MRI) Widely used FSL algorithm that calculates the percentage change in brain volume between two MRI scans of the same person at different time points. Takes under 1 hour per pair of scans. 2GB, 1 to 3 hours, single core

FSL SIENAX

NS-NDD

NS-WMD

 Study structural (MRI) Widely used FSL algorithm that calculates the normalize brain volume of an MRI scan. Takes under 1 hour per scan. 2GB, 1 to 3 hours, single core

FSL Melodic

NS-NDD

NS-WMD

 Resting State fMRI MELODIC ( Multivariate Exploratory Linear Optimized Decomposition into Independent Components ) 3.0 uses Independent Component Analysis to decompose a single or multiple 4D data sets into different spatial and temporal components. 2GB, 1 to 3 hours, single core

FSL ProbtrackX2

NS-NDD

NS-WMD

 Probabilistic tracking with crossing fibres

ProbtrackX2 repetitively samples from the distributions of voxel-wise principal diffusion directions, each time computing a streamline through these local samples to generate a probabilistic streamline or a sample from the distribution on the location of the true streamline.

 2GB, 24 to 48 hours, single core

FSL fnirt

NS-NDD

NS-WMD

 Non linear registration Non linear registration between two image volumes. 1GB, 20 minutes, single core

MIPAV

NS-NDD

NS-WMD

NS-PSY

 Analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy MIPAV enables quantitative analysis of medical images. Available

MNI LIBRARES

NS-NDD

NS-WMD

(NS-PSY)

 Pre-processing of MR images for a better and refined imaging markers extraction. These packages (e.g. dcm2mnc, dcm2nii, mincinfo, mincmath, mincresample, N3) are suited for MRI structural analysis. They allow the MANAGEMENT, conversion and visualization of different file formats. Available

SPM-LST NS-WMD A fully automated software to segment White Matter Lesions and estimate brain tissue volumes using a combination of FLAIR and 3D T1 weighted images Available on the internet 2GB, 1 to 3 hours, single core

CASCADE NS-WMD A fully automated software to segment White Matter Lesions and estimate brain tissue volumes using any combination of FLAIR, T1, T2, and PD images Newly developed algorithm 2GB, 1 to 3 hours, single core

Lesion TOADS NS-WMD Automatic detection of white matter lesions Widely distributed algorithm 12GB, 3 to 5 hours, single core

kNN-Tissue Type Prior

NS-WMD Automatic detection of white matter lesions Newly developed algorithm 12GB, 12 to 20 hours, single core

AdaBoost

 NS-NND Cross sectional hippocampal volume Newly developed algorithm for hippocampal volume based on training AdaBoost. Uses LONI resources. Contact N4U

CLASP-CIVET

NS-NDD

NS-WMD

 Cortical Thinning CIVET is a fully automatic imaging- processing pipeline focused on extraction of cortical thickness in the human brain from MRI data

2GB, 2 to 3 days, single core

BRAINVISA

NS-NDD

(NS-WMD

NS-PSY)

Segmentation of T1-weighted MR images

A modular and customizable software platform that hosts heterogeneous tools. The main toolboxes are: T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, functional MRI, nuclear imaging, EEG and magnetoencephalography, and transcranial magnetic stimulation

 Available

R

NS-NDD

NS-WMD

(NS-PSY)

Tool that deals with the problem of interpretations of significant results from populations of analyzed subjects

A free software environment for statistical computing and graphics.

 Available

OCTAVE

NS-NDD

NS-WMD

(NS-PSY)

Tool that deals with the problem of interpretations of significant results from populations of analyzed subjects

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.

Available

ITK - VTK

NS-NDD

NS-WMD

(NS-PSY)

Study of registration and correct segmentation of multidimensional imaging data and brain structures

Libraries with an extensive suite of software tools for image analysis

 Available

SPM-VBM

NS-NDD

NS-WMD

NS-PSY

Voxel Based Morphometry

SPM is a statistical technique for examining differences in brain activity recorded during functional neuroimaging experiments using neuroimaging technologies such as fMRI or PET. Furthermore, SPM can be used also to perform image pre-processing, statistical comparision and graphical representations.

Available Contact N4U

AFNI - SUMA

NS-NDD

NS-WMD

NS-PSY

Analysis of Functional NeuroImages and cortical outputs

AFNI is a used for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. SUMA is a program that adds cortical surface based functional imaging analysis to the AFNI suite of programs. It allows viewing 3D cortical surface models, and mapping volumetric data onto them.

 Available

Image-J

NS-NDD

NS-WMD

NS-PSY

Subject image visualization and analysis

ImageJ can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats. It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations can be performed in parallel with other operations.

 Available

ITK-SNAP

NS-NDD

(NS-WMD

NS-PSY)

ITK-SNAP is a software application for medical T13D image segmentation

ITK-SNAP primary use is for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.

Available

 

3D-Slicer

NS-NDD

NS-WMD

NS-PSY

Multi-modality Image analysis and visualization including: MRI, CT, DTI, fMRI, nuclear medicine.

3D-Slicer provides a graphical user interface to interact with the data. In addition to manual segmentation and the creation of 3D surface models from conventional MRI images, Slicer has also been used for non-rigid image registration and to incorporate models of the neurovascular bundle using image segmentation in MRI-guided interventions.

 Available

N4U SOFTWARE PORTFOLIO for the neuroscience community.