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

An end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line.

Proper citation: GAMBIT (RRID:SCR_009483) Copy   

•   Source: SciCrunch Registry

http://www.gimias.org

A workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology.

Proper citation: GIMIAS (RRID:SCR_009545) 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

https://hub.docker.com/r/kaczmarj/neurodocker/

Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12.

Proper citation: Neurodocker (RRID:SCR_017426) Copy   

•   Source: SciCrunch Registry

http://signalml.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.

Proper citation: signalml.org (RRID:SCR_003383) 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

http://csg.sph.umich.edu//abecasis/MACH/index.html

A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Proper citation: MACH 1.0 (RRID:SCR_001759) Copy   

•   Source: SciCrunch Registry

http://brainproducts.com/productdetails.php?id=17

Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

Proper citation: BrainVision Analyzer (RRID:SCR_002356) Copy   

•   Source: SciCrunch Registry

http://rtimage.sourceforge.net/

Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.

Proper citation: RT Image (RRID:SCR_002535) Copy   

•   Source: SciCrunch Registry

http://www.neurobs.com/

Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.

Proper citation: Presentation (RRID:SCR_002521) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/marcocongedo/software/nica

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.

Proper citation: Normative Independent Component Analysis (RRID:SCR_002506) Copy   

•   Source: SciCrunch Registry

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

http://www.nitrc.org/projects/cmind_2014/

A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans.

Proper citation: C-MIND Database (RRID:SCR_014094) Copy   

•   Source: SciCrunch Registry

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

A diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity. They provide high angular resolution (HARDI) reconstruction from DTI data with at least 20 gradient directions acquisitions.

Proper citation: Imeka Tractography Service (RRID:SCR_014124) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

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

Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.

Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy   

•   Source: SciCrunch Registry

https://github.com/BRAINSia/BRAINSTools

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

Proper citation: BRAINSCortex (RRID:SCR_001082) Copy   

•   Source: SciCrunch Registry

https://www.slicer.org/slicerWiki/index.php/Slicer4:VMTK

Provides series of modules which enable functions of Vascular Modeling Toolkit in 3D Slicer. Functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.VMTK is available through the extension manager for 3D Slicer from version 4.6.2. Main difference to Slicer3 version is that now all VMTK modules come as one extension bundle. This should enhance the installation experience for users.

Proper citation: VMTK in 3D Slicer (RRID:SCR_002579) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/bctnet/comparison/nbs

Matlab toolbox for testing hypotheses about the human connectome. NBS has been widely used to identify connections and networks comprising the connectome that are associated with an experimental effect or a between-group difference. User provides a series of connectivity matrices from different cohorts, or from the same subject during different experimental conditions. Connectivity matrices are inferred from neuroimaging data using other packages that, for example, count the number of tractography streamlines that interconnect each pair of regions (diffusion-MRI), or measure the extent of inter-regional correlation in BOLD response (fMRI). User specifies hypothesis to be tested at every connection with the general linear model. Features include: graphical user interface; NBSview, a basic network viewer modeled on SPMresults; exchange blocks for repeated measures; options to measure network size with intensity or extent; false discovery rate (FDR) option. Developed by Zalesky, Fornito, Cocchi and Bullmore.

Proper citation: Network Based Statistic Toolbox (RRID:SCR_002454) Copy   

•   Source: SciCrunch Registry