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