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

Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc.

Proper citation: Quantitative Diffusion Tools (RRID:SCR_002527) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

Proper citation: 3D Interactive Chemical Shift Imaging (RRID:SCR_002581) Copy   

•   Source: SciCrunch Registry

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

This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons, but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases (borrowed from other software) to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition, it will output statistics for each surviving cluster, and the image as a whole. Feedback would be much appreciated.

Proper citation: Cluster reporter (RRID:SCR_002218) Copy   

•   Source: SciCrunch Registry

http://fmri.wfubmc.edu/cms/software#WFU_Pipeline

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. A fully automated software application for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. Requirements: * MATLAB 7.3 or greater with the Image Processing Toolbox * SPM5

Proper citation: WFU Pipeline (RRID:SCR_002614) Copy   

•   Source: SciCrunch Registry

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

This script will take any .img file and correct it based on a cluster extent, cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately, and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox.

Proper citation: Cluster Extent Correction (RRID:SCR_002226) Copy   

•   Source: SciCrunch Registry

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

A tool that measures surface to surface distance between two triangle meshes using user-specified uniform sampling. Thus, users can choose finer sampling level to calculate errors to gain more accuracy in theerror space, or sparser sampling to gain speed and get an approximate feeling of error distribution between boundaries. Besides its pleasant visualization using the VTK library, MeshValmet also provides useful histogram and statistical information based on the sample errors, such as mean and median distance, root mean square distance, mean square distance, mean absolute distance, Hausdorff distance, 95 percentile, 68 percentile, etc. MeshValmet is based on the work of Nicolas Aspert, etc.: MESH: Measuring Errors between Surfaces using the Hausdorff distance in the proceedings of the IEEE Int. Conf. on Multimedia and Expo 2002 (ICME), vol. I, pp. 705-708. The calculation of the Dice's Coefficient is calculated by Joshua Stough using the concept of a Riemannian sum.

Proper citation: MeshValmet: Validation Metric for Meshes (RRID:SCR_006622) Copy   

•   Source: SciCrunch Registry

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

A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University).

Proper citation: JIST: Java Image Science Toolkit (RRID:SCR_008887) Copy   

•   Source: SciCrunch Registry

http://www.epilepsiae.eu/project_outputs/epilab_software

A Matlab-based software package developed for supporting researchers in performing studies on the prediction of epileptic seizures. It provides an intuitive and convenient graphical user interface. Fundamental concepts that are crucial for epileptic seizure prediction studies were implemented.This includes, for example, the development and statistical validation of prediction methodologies in long-term continuous recordings. Seizure prediction is usually based on electroencephalography (EEG) and electrocardiography (ECG) signals. EPILAB is able to process both EEG and ECG data stored in different formats. More than 35 time and frequency domain measures (features) can be extracted based on univariate and multivariate data analysis. These features can be post-processed and used for prediction purposes. The predictions may be conducted based on optimized thresholds or by applying classifications methods such as artificial neural networks, cellular neuronal networks, and support vector machines.

Proper citation: EPILAB (RRID:SCR_009573) Copy   

•   Source: SciCrunch Registry

http://www.imagevis3d.org/

A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators.

Proper citation: ImageVis3D (RRID:SCR_009566) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/draw3d/

Draw3D is a 3D rendering tool written entirely in VTK-TCL script. It is intended for fast command line rendering and visual inspection of datasets commonly found in medical imaging. It also allows the generation of images for reports or videos. As it is based on pure VTK, it can render whatever VTK can render, and runs wherever VTK can run. Meshinator is a simpler tool that uses VTKs isosurface functions to generate meshes from volumetric data. Please see the wiki for documentation

Proper citation: Draw3D and Meshinator (RRID:SCR_009444) Copy   

•   Source: SciCrunch Registry

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

A nice sign of bias field correction (nonuniformity) in medical images. This tool is fast and efficient. Technical details can be found at http://zheng.vision.googlepages.com/biasCorrection_miccai09_Zheng.pdf

Proper citation: NICE-SIGN (RRID:SCR_009629) Copy   

•   Source: SciCrunch Registry

http://www.gtec.at/Products/Software/g.BSanalyze-Specs-Features

An interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain-, heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines, event-related ECG, support for P300 and SSVEP/SSSEP BCIs, zero class detection for BCIs, compressed spectral array, minimum energy, and more! g.BSanalyze consists of a base version for data import, visualization, transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets, including P300, SSVEP, motor imagery, CSP BCIs, Tilt-Table, EPs, multi-unit activity, CFM, and ERD/ERS.

Proper citation: g.BSanalyze (RRID:SCR_009625) 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://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

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

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://software.incf.org/

Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added.

Proper citation: INCF Software Center (RRID:SCR_002347) Copy   

•   Source: SciCrunch Registry

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

A reference for modifications, extensions, and utilities for the FMRIB Software Library (FSL).

Proper citation: FSL extensions (RRID:SCR_009472) Copy   

•   Source: SciCrunch Registry

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

A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd).

Proper citation: DICOMConvert (RRID:SCR_014100) Copy   

•   Source: SciCrunch Registry

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

Standalone software designed to be used by radiology researchers for storage and anonymization of research images.

Proper citation: Notion ResearchPACS (RRID:SCR_014154) Copy   

•   Source: SciCrunch Registry