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

The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.

Proper citation: DualSurfaceMin (RRID:SCR_008278) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/SVT

Software tool for determining the statistically significant regions of activation in single or multi-subject human brain functional studies. It can be also applied to structural brain data for analyzing developmental, dementia and other changes of anatomy over time. This package was originally developed to work on Sun SPARC and SGI stations using the "C" language compiler provided by Sun/SGI as part of the standard system software.

Proper citation: Sub-Volume Thresholding Analysis (RRID:SCR_008272) Copy   

•   Source: SciCrunch Registry

http://loni.usc.edu/Software/CFMBIS

A computer-aided tool for 2-D brain image segmentation using an electrostatic charged fluid model. It allows researchers to perform 2-D image segmentation in brain MR image data. Each interactive visualization element corresponding to the embedded function enables the end user to easily manipulate the image data. The visual environment of this tool provides an easy-to-use means of inspection and interpretation of image data using the LONI jViewbox library. CFMBIS uses the Java Image I/O plug-in architecture to read a wide variety of common medical image file formats.

Proper citation: Charged Fluid Model for Brain Image Segmentation (RRID:SCR_008281) Copy   

•   Source: SciCrunch Registry

http://neurodata.io/

Project portal dedicated to understand animal and machine intelligence and repository of data and tools. Suite of tools to analyze and graph imaging data. Image and data repository for large, publicly available neuro-specific data files and images. Contains tools for analytics, databases, cloud computing, and Web-services applied to both big neuroimages and big neurographs.

Proper citation: neurodata (RRID:SCR_014264) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ap_seg_2013_nih/

A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet.

Proper citation: NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) Copy   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://users.loni.ucla.edu/~shattuck/brainsuite/

Suite of image analysis tools designed to process magnetic resonance images (MRI) of the human head. BrainSuite provides an automatic sequence to extract genus-zero cortical surface mesh models from the MRI. It also provides a set of viewing tools for exploring image and surface data. The latest release includes graphical user interface and command line versions of the tools. BrainSuite was specifically designed to guide its users through the process of cortical surface extraction. NITRC has written the software to require minimal user interaction and with the goal of completing the entire process of extracting a topologically spherical cortical surface from a raw MR volume within several minutes on a modern workstation. The individual components of BrainSuite may also be used for soft tissue, skull and scalp segmentation and for surface analysis and visualization. BrainSuite was written in Microsoft Visual C using the Microsoft Foundation Classes for its graphical user interface and the OpenGL library for rendering. BrainSuite runs under the Windows 2000 and Windows XP Professional operating systems. BrainSuite features include: * Sophisticated visualization tools, such as MRI visualization in 3 orthogonal views (either separately or in 3D view), and overlayed surface visualization of cortex, skull, and scalp * Cortical surface extraction, using a multi-stage user friendly approach. * Tools including brain surface extraction, bias field correction, voxel classification, cerebellum removal, and surface generation * Topological correction of cortical surfaces, which uses a graph-based approach to remove topological defects (handles and holes) and ensure a tessellation with spherical topology * Parameterization of generated cortical surfaces, minimizing a harmonic energy functional in the p-norm * Skull and scalp surface extraction

Proper citation: BrainSuite (RRID:SCR_006623) Copy   

•   Source: SciCrunch Registry

http://martinos.org/mne/

Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.

Proper citation: MNE software (RRID:SCR_005972) Copy   

•   Source: SciCrunch Registry

http://www.slicer.org/slicerWiki/index.php/Slicer3:Module:Rician_Noise_Removal

Two Slicer3 modules removing rician noise in diffusion tensor MRI

Proper citation: Slicer3 Module Rician noise filter (RRID:SCR_009614) Copy   

•   Source: SciCrunch Registry

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

Software that uses a novel statistical-learning technique to segment brain regions of interest (ROIs) based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.

Proper citation: LONI Brain Parser (RRID:SCR_009572) Copy   

•   Source: SciCrunch Registry

https://github.com/UCSFBiomagneticImagingLab/nutmeg

Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Proper citation: NUTMEG (RRID:SCR_002748) Copy   

•   Source: SciCrunch Registry

http://www.xnat.org

Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.

Proper citation: XNAT - The Extensible Neuroimaging Archive Toolkit (RRID:SCR_003048) Copy   

•   Source: SciCrunch Registry

https://bioimagesuiteweb.github.io/webapp/index.html

Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

Proper citation: BioImage Suite (RRID:SCR_002986) Copy   

•   Source: SciCrunch Registry

http://bio3d.colorado.edu/imod

A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X

Proper citation: IMOD (RRID:SCR_003297) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/MAST.html

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry

https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

•   Source: SciCrunch Registry

https://github.com/FeeLab/seqNMF

Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers.

Proper citation: seqNMF (RRID:SCR_017068) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/itk-snap/

Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Proper citation: ITK-SNAP (RRID:SCR_002010) Copy   

•   Source: SciCrunch Registry

https://github.com/trendscenter/gift

Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki.

Proper citation: Group ICA of fMRI Toolbox (RRID:SCR_001953) Copy   

•   Source: SciCrunch Registry

http://neuroimage.usc.edu/brainstorm/

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

Proper citation: Brainstorm (RRID:SCR_001761) Copy   

•   Source: SciCrunch Registry