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http://labs.nri.ucsb.edu/reese/benjamin/SA3D.html

A user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.

Proper citation: Spatial Analysis 3D (RRID:SCR_002563) Copy   

•   Source: SciCrunch Registry

http://www.cise.ufl.edu/~tichen/ShapeComplexAtlas.zip

A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012

Proper citation: ShapeComplexAtlas (RRID:SCR_002553) Copy   

•   Source: SciCrunch Registry

http://www.na-mic.org/Wiki/index.php/UNC_SPHARM-PDM_Tutorial

Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Proper citation: SPHARM-PDM Toolbox (RRID:SCR_002546) Copy   

•   Source: SciCrunch Registry

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

A stand-alone axecutable under all main Windows OS for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However, it can be used purposefully by people of any age, including adult and elderly. This application features highest graphic quality, a powerful adaptive engine for the difficulty level, a database of users and statistical tools to evaluate the progress. Currently English, French and Italian are supported, but any language can be easily supported.

Proper citation: Working Memory Trainer (RRID:SCR_002617) Copy   

•   Source: SciCrunch Registry

http://scikit-learn.org/

scikit-learn: machine learning in Python

Proper citation: scikit-learn (RRID:SCR_002577) Copy   

•   Source: SciCrunch Registry

http://nifti.nimh.nih.gov/

Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools

Proper citation: Neuroimaging Informatics Technology Initiative (RRID:SCR_003141) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/ProvenanceEditor

A self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

Proper citation: LONI Provenance Editor (RRID:SCR_002483) Copy   

•   Source: SciCrunch Registry

http://tarquin.sourceforge.net/

An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.

Proper citation: TARQUIN (RRID:SCR_002598) Copy   

•   Source: SciCrunch Registry

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

A Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr

Proper citation: DICOM UploadGUI (RRID:SCR_009458) Copy   

•   Source: SciCrunch Registry

http://fmripower.org

An easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data.

Proper citation: FMRIpower (RRID:SCR_009576) Copy   

•   Source: SciCrunch Registry

http://www.ant-neuro.com/products/eeprobe

A complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser. ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X.

Proper citation: EEProbe (RRID:SCR_009570) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/software.cfm?ID=101

Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime.

Proper citation: E-Prime Extensions for fMRI (RRID:SCR_009568) Copy   

•   Source: SciCrunch Registry

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

This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required). The software can be built as either a stand-alone or a CLI plugin for 3D Slicer.

Proper citation: Finsler tractography module for Slicer (RRID:SCR_009477) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DiD

Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner.

Proper citation: LONI De-identification Debablet (RRID:SCR_009593) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/231-biomesh3d.html

A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.

Proper citation: BioMesh3D (RRID:SCR_009534) Copy   

•   Source: SciCrunch Registry

http://besa.de

Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI.

Proper citation: BESA (RRID:SCR_009530) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hitachi2nirs/

A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file.

Proper citation: Hitachi2nirs (RRID:SCR_009494) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/mrilateralventricle/

A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject.

Proper citation: ALVIN (RRID:SCR_009527) Copy   

•   Source: SciCrunch Registry

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

Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated.

Proper citation: fMRI-CPCA (RRID:SCR_009520) Copy   

•   Source: SciCrunch Registry

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

An end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line.

Proper citation: GAMBIT (RRID:SCR_009483) Copy   

•   Source: SciCrunch Registry