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http://www.brainvisa.info/

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

Proper citation: BrainVISA / Anatomist (RRID:SCR_007354) Copy   

•   Source: SciCrunch Registry

http://fmri.wfubmc.edu/software/PickAtlas

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WFU PickAtlas (RRID:SCR_007378) Copy   

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http://mipav.cit.nih.gov

A Java-based application that enables quantitative analysis and visualization of medical images of numerous modalities such as DTI, PET, MRI, CT, or microscopy. Using MIPAV's standard user-interface and analysis tools, researchers at remote sites (via the internet) can easily share research data and analyses, thereby enhancing their ability to research, diagnose, monitor, and treat medical disorders. MIPAV can be run on any Java-enabled platform such as Windows, UNIX, or Macintosh OS X. Functionality includes segmentation, inter- and intra multi-modality registration, surface rendering, volume rendering and reading and writing a large number of biomedical file formats including: DICOM 3.0, Analyze, NIFTI, SPM, MINC, Phillips, GE, Zeiss, Biorad, jpeg, png, tiff, mrc, fits, interfile, and many more.

Proper citation: MIPAV: Medical Image Processing and Visualization (RRID:SCR_007371) Copy   

•   Source: SciCrunch Registry

http://www.alivelearn.net/xjview8/

A viewing program for Statistical Parametric Mapping (SPM2, SPM5 and SPM8). p-value slider, displays multiple images at a time and can be used to build Region of Interest (ROI) masks. For a given region you can find the anatomical name and search the selected region in online database (wiki, Google scholar and PubMed).

Proper citation: xjView: A Viewing Program For SPM (RRID:SCR_008642) Copy   

•   Source: SciCrunch Registry

http://www.ant-neuro.com/products/asa

A highly flexible EEG/ERP and MEG analysis package with a variety of source reconstruction, signal analysis and MRI processing features. ASA combines functional brain imaging with the visualization and incorporation of morphological information obtained from MRI or CT. ASA is a highly interactive and flexible software tool that can be applied to neuro-physiological and clinical brain research. ASA gives a realistic impression of your experimental configuration together with topographical mapping of EEG and MEG and the results of your analysis. ASA is developed for and by people dedicated to brain research. The concept of flexibility and openness covers even most complex analysis demands. The ASA environment is particularly attractive for those that wish to develop their own methods in third party packages like Matlab and use ASA for pre-processing and visualization purposes.

Proper citation: ASA - Advanced Source Analysis (RRID:SCR_012867) 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

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

A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.

Proper citation: libSBML (RRID:SCR_014134) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mrml-paraview/

ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView.

Proper citation: KWScene: MRML-based Atlas and Scene Builder/Reader/Writer (RRID:SCR_014131) Copy   

•   Source: SciCrunch Registry

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

Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods.

Proper citation: MARS (Multi-Atlas Robust Segmentation) (RRID:SCR_014137) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/minc-toolkit

A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp.

Proper citation: minc-toolkit (RRID:SCR_014138) Copy   

•   Source: SciCrunch Registry

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

Brainnetome Atlas Viewer shows the anatomical connectivity-based parcellation results, including the maximum probabilistic maps, probabilistic maps and both the anatomical and functional connectivity patterns, which have been developed in Brainnetome Center, CASIA. The atlas is based on the analysis of connectional architecture with in vivo multi-modal MRI data.

Proper citation: Brainnetome Atlas Viewer (RRID:SCR_014091) Copy   

•   Source: SciCrunch Registry

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

A clinical toolbox useful for normalizing data from individuals with brain injury and/or modalities popular in the clinical environment (CT). It supports either enantiomorphic or lesion-masked normalization. It can be either scripted or used with SPM's simple graphical interface.

Proper citation: Clinical Toolbox for SPM (RRID:SCR_014096) Copy   

•   Source: SciCrunch Registry

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

A tool which computes an automatic segmentation of neonatal brain MRI. It uses a registered probabilistic brain atlas to select training samples and to be used as a spatial prior.

Proper citation: Neoseg (RRID:SCR_014144) Copy   

•   Source: SciCrunch Registry

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

This tool allows segmenting neonate brain MRI using a subject-specific atlas. It generates a subject-specific atlas based on an atlas population and some diffusion images of the subject to segment. Then a single atlas method is run with this atlas to obtain results.

Proper citation: NeoSegPipeline (RRID:SCR_014145) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/neuron-c/

A simulation language for modeling biophysically realistic neural circuits (1 to 10,000 neurons) and simulating physiology experiments on it. Programs for plotting and displaying data are included.

Proper citation: Neuron-C (RRID:SCR_014148) Copy   

•   Source: SciCrunch Registry

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

A database which contains longitudinal structural MRIs, spectroscopy, DTI and correlated clinical/behavioral data from approximately 500 healthy, normally developing children, ages newborn to young adult.

Proper citation: NIH Pediatric MRI Data Repository (RRID:SCR_014149) Copy   

•   Source: SciCrunch Registry

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

A tool which offers a fast algorithm for computing myelin maps from multiecho T2 relaxation data using parallel computation with multicore CPUs and graphics processing units (GPUs). The tool also provides non-local spatial regularization to produce more accurate and reliable myelin maps for noisy T2 relaxation data.

Proper citation: Fast T2 relaxation data analysis with stimulated echo correction and non-local spatial regularisation (RRID:SCR_014108) Copy   

•   Source: SciCrunch Registry

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

A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain.

Proper citation: ERPwavelab (RRID:SCR_014106) Copy   

•   Source: SciCrunch Registry

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

A functional connectivity analysis tool for near-infrared spectroscopy data. Its functions include preprocessing, quality control, FC calculation and network analysis.

Proper citation: Functional Connectivity Analysis Tool for near-infrared spectroscopy data (RRID:SCR_014111) Copy   

•   Source: SciCrunch Registry

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

A toolbox for a point-process derived GLM analysis of eye tracking data in Matlab. Data loading, model specification, fitting and review are organized into a sequence of events, each of which is handled by a separate module in the toolbox. The graphical interface was created using the Matlab graphical user interface development environment.

Proper citation: GazeReader (RRID:SCR_014112) Copy   

•   Source: SciCrunch Registry