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http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://nrg.wustl.edu/software/dicom-browser/

A platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. DicomBrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation.

Proper citation: DicomBrowser (RRID:SCR_000864) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/imcalc/

A collection of functions with batch functionality for SPM: * user entered expression (one set of volumes); * binarize non-zero voxels; * binarize/threshold each image; * binarize non-zero voxels, sum, rebinarize; * voxelwise calculations on pairs (add sub mult div ... etc.); * flip sign of all non-zero voxels; * x-flip image along y = 0; * mask images to a template; * T-to-Z transform; * Winsorize (cap) extreme values; * Z-score transform of image relative to its global mean and SD; * write single voxels to a .nii; * create a cluster image; * split cluster image into constituent images; * write hemisphere masks from template; * homotopic calculations; * replace zeros with __; * pad image with extra voxels;

Proper citation: imcalc: SPM batch image calculator (RRID:SCR_000868) Copy   

•   Source: SciCrunch Registry

http://neuralensemble.org/trac/OpenElectrophy

Software Python module for electrophysiology data analysis.

Proper citation: OpenElectrophy (RRID:SCR_000819) Copy   

•   Source: SciCrunch Registry

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

A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program 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: BRAINSCut (RRID:SCR_000861) Copy   

•   Source: SciCrunch Registry

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

A cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device.

Proper citation: GesTr (RRID:SCR_000857) Copy   

•   Source: SciCrunch Registry

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

Generic classification tool for 3D images

Proper citation: COMPARE (RRID:SCR_000855) Copy   

•   Source: SciCrunch Registry

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

A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand.

Proper citation: Data Format Tools (RRID:SCR_000856) Copy   

•   Source: SciCrunch Registry

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

A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

Proper citation: LONI Pipeline Processing Environment (RRID:SCR_001161) Copy   

•   Source: SciCrunch Registry

http://www.itk.org

Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Segmentation and Registration Toolkit (RRID:SCR_001149) Copy   

•   Source: SciCrunch Registry

https://nda.nih.gov/

The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Proper citation: NIMH Data Archive (RRID:SCR_004434) Copy   

•   Source: SciCrunch Registry

https://www.fieldtriptoolbox.org

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

Proper citation: FieldTrip (RRID:SCR_004849) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/

TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.

Proper citation: TrackVis (RRID:SCR_004817) Copy   

•   Source: SciCrunch Registry

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

Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter.

Proper citation: VectorValuedHistogramNormalizer (RRID:SCR_000082) Copy   

•   Source: SciCrunch Registry

https://dipy.org/

Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.

Proper citation: Dipy (RRID:SCR_000029) Copy   

•   Source: SciCrunch Registry

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

A sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a stable structure of reference can be used without the simple best fit of all surfaces.

Proper citation: CMFreg (RRID:SCR_000171) Copy   

•   Source: SciCrunch Registry

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

OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

Proper citation: MIView (RRID:SCR_000413) Copy   

•   Source: SciCrunch Registry

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

Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results.

Proper citation: RapidArt (RRID:SCR_000422) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/brainfx/

A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces.

Proper citation: BrainFX (RRID:SCR_000302) Copy   

•   Source: SciCrunch Registry

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

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry