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http://www.xinapse.com/

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.

Proper citation: Jim (RRID:SCR_009589) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/hispeedpackets/

HI-SPEED Software Packets contain # unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques, # 2-dimensional and 3-dimensional analytical (Shepp-Logan) magnetic resonance imaging phantoms in both the Fourier and image domains, # techniques for reporting the underlying signal-to-noise ratio in magnetic resonance (MR) images, # 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 # 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.

Proper citation: HI-SPEED Software Packets (RRID:SCR_009585) Copy   

•   Source: SciCrunch Registry

http://www.bsl.ece.vt.edu/index.php?page=ara-dataset

Dataset of structural MR images of 70 subjects collected during 2008-2010 across a wide range of ages. The dataset also contains resting state fMRI for most subjects. The structural images are T1 weighted, T2 weighted-FLAIR, 25 direction DTI, and the T1 mapping DESPOT [1] sequence. Reconstructed T1 maps for each subject are also available. The aquisition protocol was designed to study structural differences between young and older adults including both shape and intensity changes. Anonymized DICOM image sessions and processed images for each subject are available. The data is licensed under the Creative Commons Attribution License. It may be used freely for commercial, academic, or other use, as long as the original source is properly cited. http://www.bsl.ece.vt.edu/index.php?page=ara-dataset

Proper citation: Age Related Atrophy Dataset (RRID:SCR_009528) Copy   

•   Source: SciCrunch Registry

http://amilab.org

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.

Proper citation: AMILab (RRID:SCR_009525) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/fnirs_downstate/

A data analysis environment for diffuse optical tomography (DOT) functional neuroimaging data. Developed to process data from steady-state time-series measurements, it allows for maximal flexibility in the number and positions of optodes. The central component is an application called NAVI. Features include: # An electronic ledger (records metadata for all data transformations). # Data conditioning (e.g., frequency-filtering, selection of data on the basis of signal-to-noise ratio.) # 2D or 3D image formation and display. # Interpretation: atlas-based mapping; automated anatomical labeling; GLM; data-driven methods (e.g., PCA, ICA); model-based (e.g., dynamic causal modeling) and data-driven (e.g., correlation) connectivity analysis. Another important component is the Brain Model Generator, which includes FEM meshes for all parts of the head accessible to DOT measurements. The user can input the numbers of optodes, and manually specify their locations or input tracking-system data.

Proper citation: fNIRS Data Analysis Environment (RRID:SCR_009522) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/dti_rat_atlas/

3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.

Proper citation: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) Copy   

•   Source: SciCrunch Registry

https://compumedicsneuroscan.com/products/by-name/curry/

Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package.

Proper citation: CURRY (RRID:SCR_009546) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cost_unc/

A tool that implements a graph-based connectivity assessment method. This method uses a multi-directional graph propagation method applied to sampled orientation distribution function (ODF), which can be computed directly from the original diffusion imaging data.

Proper citation: COST (RRID:SCR_014098) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/broccoli/

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

Proper citation: BROCCOLI (RRID:SCR_014093) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/afni_3dsvm/

A command-line program and plugin for AFNI built around SVM-Light. It performs support vector machine (SVM) analysis on fMRI data and runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X.

Proper citation: 3dsvm (RRID:SCR_014083) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/BrainCSI.shtml

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.

Proper citation: BrainCSI (RRID:SCR_013244) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ntu-dsi-122/

A diffusion spectrum imaging (DSI) template constructed in the standard ICBM-152 space from 122 healthy adults. The template was built through incorporating the macroscopic anatomical information using high-resolution T1-weighted images and the microscopic structural information obtained from DSI datasets, rendering it to achieve a high anatomical matching to the ICBM-152 space. This template can serve as a representative DSI dataset for a healthy adult population. It is released in its original DWI format.

Proper citation: NTU-DSI-122: a DSI template in ICBM-152 space (RRID:SCR_014155) Copy   

•   Source: SciCrunch Registry

http://www.cis.hut.fi/projects/ica/fastica/

General-purpose unsupervised data-analysis tool, most often used for brain imaging data.

Proper citation: FastICA (RRID:SCR_013110) Copy   

•   Source: SciCrunch Registry

https://github.com/NIRALUser/DTIAtlasBuilder

This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed.

Proper citation: DTI Atlas Builder (RRID:SCR_013112) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/carlsim/

A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level.

Proper citation: CARLsim: a GPU-accelerated SNN Simulator (RRID:SCR_014095) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mricros

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

Proper citation: MRIcroS (RRID:SCR_014142) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/riem_mglm/

A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.

Proper citation: Multivariate General Linear Models (MGLM) on Riemannian Manifolds (RRID:SCR_014143) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gimme/

Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.

Proper citation: GIMME (RRID:SCR_014115) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/xfsl/

A set of many useful automation scripts to facilitate the neuroimaging data analysis process. It contains BASH scripts for MRI data management, FSL automation and web application.

Proper citation: XFSL: An FSL toolbox (RRID:SCR_014181) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/psics

Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools.

Proper citation: Parallel Stochastic Ion Channel Simulator (RRID:SCR_014159) Copy   

•   Source: SciCrunch Registry