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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://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://www.loni.usc.edu/Software/LOVE

A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html

Proper citation: LONI Visualization Tool (RRID:SCR_000765) Copy   

•   Source: SciCrunch Registry

http://niftilib.sourceforge.net/pynifti/

PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.

Proper citation: PyNIfTI (RRID:SCR_000693) 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

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

https://vpixx.com/products/viewpixx/

Research-grade, CRT-replacement LCD display system for vision science and psychophysics. It combines a 22.5″ 1920×1200 industrial LCD (wide 176°/176° viewing angles) with a custom panel/video controller engineered for deterministic stimulus timing and synchronized acquisition. The display supports 12-bit intensity resolution per RGB channel via custom video modes. It uses a scanning RGB LED backlight to improve temporal precision (e.g., crisp frame transitions and reduced motion artifacts) while bypassing consumer “enhancement” processing to keep output predictable for experiments. VIEWPixx also integrates microsecond-synchronized peripherals commonly needed in timing-sensitive paradigms—24-channel TTL I/O (triggers), stereo audio I/O, analog I/O, and a button-box interface—implemented on the same board as the video pipeline for tight hardware-to-video synchronization.

Proper citation: VPixx: VIEWPixx (RRID:SCR_013271) Copy   

•   Source: SciCrunch Registry

https://vpixx.com/hardware/projector/

Unique DLP LED projector which has been designed to be the most flexible display solution for vision research and neuroscience research. The PROPixx features a native resolution of 1920 x 1080, and can be driven with refresh rate up to 500Hz with deterministic timing. The PROPixx uses high brightness LEDs as a light source, giving a wide colour gamut and much longer lifetime than halogen light sources. It features high-bit depth, up to 12-bit per color for high-frequency full colour stimulation. For stereo vision applications, our high-speed ferro-electric circular polarizer can project stereoscopic stimuli with the use of passive glasses at up to 400Hz. In addition the PROPixx includes an array of peripherals which often need to be synchronized to video during an experiment, and with perfect microsecond precision.

Proper citation: VPixx: PROPixx (RRID:SCR_013299) Copy   

•   Source: SciCrunch Registry

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

The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels: background, brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly, assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly, we built the [123I]FP-CIT SPECT template by the mean of the transformed and normalized images. More info: 1) Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2) Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage, Volume 65, 2013, pp. 449-455. http://dx.doi.org/10.1016/j.neuroimage.2...

Proper citation: FP-CIT SPECT brain template in MNI space (RRID:SCR_013668) Copy   

•   Source: SciCrunch Registry