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

This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL.

Proper citation: DW-MRI registration in FSL (RRID:SCR_009461) Copy   

•   Source: SciCrunch Registry

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

Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource.

Proper citation: DbGaP Cleaner (RRID:SCR_009462) Copy   

•   Source: SciCrunch Registry

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

This project is used for students enrolled in courses using the JIST framework. Content in this CVS is freely available, but it is not intended for any specific purpose.

Proper citation: JHU Proj. in Applied Medical Imaging (RRID:SCR_009499) Copy   

•   Source: SciCrunch Registry

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

Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications.

Proper citation: INCF Neuroimaging Data Sharing (RRID:SCR_009497) Copy   

•   Source: SciCrunch Registry

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

Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added.

Proper citation: IDeA Lab brain image processing suite (RRID:SCR_009495) Copy   

•   Source: SciCrunch Registry

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

A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group.

Proper citation: Groupwise Image Registration Toolbox (RRID:SCR_009492) Copy   

•   Source: SciCrunch Registry

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

An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies.

Proper citation: HD Neuro-Informatics (RRID:SCR_009493) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools/tree/master/BRAINSMush

Tool to generate brain volume mask from input of T1 and T2-weighted images alongside a region of interest brain mask. This volume mask omits dura, skull, eyes, etc. The program is built upon ITK and uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

Proper citation: BRAINSMush (RRID:SCR_009485) Copy   

•   Source: SciCrunch Registry

https://fitbir.nih.gov/

Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories.

Proper citation: Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/polgui/

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

Proper citation: POLGUI - Matlab Polhemus Interface (RRID:SCR_006752) Copy   

•   Source: SciCrunch Registry

https://itunes.apple.com/gb/app/neuropub-visualizer/id405721542?mt=8

A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results.

Proper citation: NeuroPub Visualizer (RRID:SCR_006797) Copy   

•   Source: SciCrunch Registry

http://scalablebrainatlas.incf.org/

A web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required). The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations. This fully web-based display engine for brain atlases and topologies allows client websites to show brain region related data in a 3D interactive context. Currently available atlases are: * Macaque: The Paxinos Rhesus Monkey atlas (2000) * Macaque: Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991), Lewis and Van Essen (2000), Regional Map from K��tter and Wanke (2005), Paxinos Rhesus Monkey (2000) * Macaque: The NeuroMaps Macaque atlas (2008) * Mouse: The INCF Waxholm Space for the mouse (2011). Previous versions available. * Mouse: The Allen Mouse Brain volumetric atlas (ABA07) * Human: The LPBA40 parcellation, registered to SRI24 space A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage. Other applications include: * Analyze atlas templates in Matlab * List all regions belonging to the given template * List of supported atlas templates * Find region by coordinate * Color-coded PNG (bitmap) or SVG (vector) image of a brain atlas slice * Region thumbnail in 2D (slice) or 3D (stack of slices) The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf K��tter in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen.

Proper citation: Scalable Brain Atlas (RRID:SCR_006934) Copy   

•   Source: SciCrunch Registry

http://bric.unc.edu/ideagroup/free-softwares/ABSORB/

This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill.

Proper citation: ABSORB: Atlas Building by Self-Organized Registration and Bundling (RRID:SCR_007018) Copy   

•   Source: SciCrunch Registry

http://www.cns.atr.jp/dni/en/downloads/tools-for-brain-behavior-data-sharing/

This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file.

Proper citation: Matlab Neuroshare Library (RRID:SCR_006957) Copy   

•   Source: SciCrunch Registry

http://omlc.ogi.edu/software/mc/

MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications.

Proper citation: MCML and CONV (RRID:SCR_002419) Copy   

•   Source: SciCrunch Registry

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

Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.

Proper citation: NPTK (RRID:SCR_002496) Copy   

•   Source: SciCrunch Registry

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

Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.

Proper citation: NITRC Enhanced Services (RRID:SCR_002494) Copy   

•   Source: SciCrunch Registry

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

Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images

Proper citation: NIRAL Utilities (RRID:SCR_002490) Copy   

•   Source: SciCrunch Registry

http://mgui.wikidot.com

An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework

Proper citation: ModelGUI (RRID:SCR_002441) Copy   

•   Source: SciCrunch Registry

http://air.bmap.ucla.edu/MultiTracer2/MultiTracer.html

A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set.

Proper citation: MultiTracer (RRID:SCR_002445) Copy   

•   Source: SciCrunch Registry