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http://pysurfer.github.com

Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PySurfer (RRID:SCR_002524) Copy   

•   Source: SciCrunch Registry

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

Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.)

Proper citation: Spanish Resting State Network (RRID:SCR_002562) Copy   

•   Source: SciCrunch Registry

http://slicedrop.com

A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ).

Proper citation: Slice:Drop (RRID:SCR_002557) Copy   

•   Source: SciCrunch Registry

http://brainmap.org/sleuth/

Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space.

Proper citation: Sleuth (RRID:SCR_002555) Copy   

•   Source: SciCrunch Registry

http://www.sdmproject.com/

Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera).

Proper citation: Signed Differential Mapping (RRID:SCR_002554) Copy   

•   Source: SciCrunch Registry

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

Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher

Proper citation: WFU Biological Parametric Mapping Toolbox (RRID:SCR_002613) Copy   

•   Source: SciCrunch Registry

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

Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command.

Proper citation: peak nii (RRID:SCR_002572) Copy   

•   Source: SciCrunch Registry

http://www.vaa3d.org

A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.

Proper citation: Vaa3D (RRID:SCR_002609) Copy   

•   Source: SciCrunch Registry

http://www.trianglebiosystems.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software

Proper citation: Triangle BioSystems (RRID:SCR_002603) Copy   

•   Source: SciCrunch Registry

http://www.tractor-mri.org.uk/

Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.

Proper citation: TractoR: Tractography with R (RRID:SCR_002602) Copy   

•   Source: SciCrunch Registry

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

An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left.

Proper citation: TetraMetrix (RRID:SCR_002601) Copy   

•   Source: SciCrunch Registry

http://tipl.labsolver.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM)

Proper citation: Template Image Processing Library (RRID:SCR_002600) Copy   

•   Source: SciCrunch Registry

http://www.turtleseg.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process.

Proper citation: TurtleSeg (RRID:SCR_002605) Copy   

•   Source: SciCrunch Registry

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

Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325

Proper citation: PHYCAA+: adaptive physiological noise correction for BOLD fMRI (RRID:SCR_002514) Copy   

•   Source: SciCrunch Registry

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

A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

Proper citation: PennCNV (RRID:SCR_002518) Copy   

•   Source: SciCrunch Registry

https://pdbp.ninds.nih.gov

Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders.

Proper citation: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) Copy   

•   Source: SciCrunch Registry

http://idealab.ucdavis.edu/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks.

Proper citation: Subject Library (RRID:SCR_002595) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/panda-tool/

Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface).

Proper citation: PANDA (RRID:SCR_002511) Copy   

•   Source: SciCrunch Registry

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

A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).

Proper citation: TAPIR (RRID:SCR_002596) Copy   

•   Source: SciCrunch Registry

http://sve.bmap.ucla.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.

Proper citation: Segmentation Validation Engine (RRID:SCR_002591) Copy   

•   Source: SciCrunch Registry