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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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M3 Resource Report Resource Website 1+ mentions |
M3 (RRID:SCR_002475) | M3 | data processing software, image processing software, software application, software resource | A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:22008370 | Free, Available for download, Freely available | nlx_155877 | SCR_002475 | Multi-modal imaging and multi-level characteristic with multi-classifier | 2026-09-19 12:50:01 | 2 | ||||||
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RT Image Resource Report Resource Website 10+ mentions |
RT Image (RRID:SCR_002535) | RT_Image | software application, software resource | 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. | computed tomography, magnetic resonance, optical imaging, pet, spect, mri, dicom |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford University School of Medicine; California; USA |
PMID:17375973 | Free, Available for download, Freely available | nlx_155940 | http://www.nitrc.org/projects/rt_image | SCR_002535 | 2026-09-19 12:50:00 | 10 | ||||||
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ROBEX Resource Report Resource Website 1+ mentions |
ROBEX (RRID:SCR_002534) | ROBEX | data processing software, image analysis software, image processing software, segmentation software, software application, software resource | An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts. | magnetic resonance, mri, skull stripping, classification, segmentation, brain, skull | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:21880566 | Free, Available for download, Freely available | nlx_155939 | http://www.nitrc.org/projects/robex | SCR_002534 | Robust Brain Extraction (ROBEX), Robust Brain Extraction | 2026-09-19 12:50:00 | 3 | |||||
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REX Resource Report Resource Website 10+ mentions |
REX (RRID:SCR_002532) | REX | data processing software, image analysis software, software application, software resource, software toolkit | A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial. | analyze, linux, macos, matlab, magnetic resonance, nifti, posix/unix-like, time domain analysis, visualization, workflow, region of interest, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center is related to: Biositemaps |
Free, Available for download, Freely available | nlx_155937 | http://www.nitrc.org/projects/rex | http://www.neuroimaging.org.au/nig/rex | SCR_002532 | 2026-09-19 12:50:00 | 42 | ||||||
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R-package for adaptive DWI analysis Resource Report Resource Website |
R-package for adaptive DWI analysis (RRID:SCR_002528) | R-package for adaptive DWI analysis | data processing software, image processing software, software application, software resource | The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures. | afni brik, analyze, console (text based), dicom, fortran, macos, microsoft, magnetic resonance, nifti, posix/unix-like, r, diffusion weighted, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
Free | nlx_155934 | SCR_002528 | 2026-09-19 12:50:00 | 0 | ||||||||
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Source Information Flow Toolbox Resource Report Resource Website 1+ mentions |
Source Information Flow Toolbox (RRID:SCR_002561) | SIFT | data processing software, data visualization software, image analysis software, segmentation software, software application, software resource, software toolkit | A GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location. | connectivity analysis, directed transfer analysis, eeg, meg, electrocorticography, granger causality, partial directed coherence |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: EEGLAB has parent organization: Swartz Center for Computational Neuroscience |
Free, Available for download, Freely available | nlx_155967 | http://www.nitrc.org/projects/sift | SCR_002561 | 2026-09-19 12:50:00 | 3 | |||||||
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Brain lesion segmentation tool using SVM Resource Report Resource Website |
Brain lesion segmentation tool using SVM (RRID:SCR_002583) | Brain lesion segmentation tool using SVM | data processing software, image analysis software, segmentation software, software application, software resource | Segmentation tool that uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation. Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response. | magnetic resonance, brain lesion, image analysis, machine learning, support vector machine |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:23303595 | Free, Available for download, Freely available | nlx_155988 | SCR_002583 | Brain lesion segmentation tool using Support Vector Machines | 2026-09-19 12:50:01 | 0 | ||||||
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Fast Nonlocal Means for MRI denoising Resource Report Resource Website |
Fast Nonlocal Means for MRI denoising (RRID:SCR_002586) | Fast Nonlocal Means for MRI denoising | data processing software, image processing software, software application, software resource | A fast and robust software implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images. They use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone: http://www.nitrc.org/snapshots.php?group_id=518 | analyze, artifact removal, c++, filtering, frequency domain, intensity non-uniformity correction, intensity operation, linux, macos, microsoft, minc, magnetic resonance, nifti, nrrd, other unix-like, posix/unix-like, quality metrics, spatial transformation, nonlocal means, nlm, c++, itk, mri, denoising |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer |
Free, Available for download, Freely available | nlx_155991 | SCR_002586 | 2026-09-19 12:50:01 | 0 | ||||||||
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vis: SPM Visualized Statistics toolbox Resource Report Resource Website 1+ mentions |
vis: SPM Visualized Statistics toolbox (RRID:SCR_002619) | vis | data processing software, image analysis software, software application, software resource, software toolkit | Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox. | analyze, magnetic resonance, nifti, quantification, statistical operation, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: National University of Singapore; Singapore; Singapore |
Free, Available for download, Freely available | nlx_156024 | http://www.nitrc.org/projects/vis | SCR_002619 | Visualized Statistics toolbox (vis), Visualized Statistics toolbox, vis: visualized statistics toolbox | 2026-09-19 12:50:02 | 3 | ||||||
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XCEDE Schema Resource Report Resource Website 1+ mentions |
XCEDE Schema (RRID:SCR_002571) | XCEDE | data management software, software application, software resource | Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit. | computed tomography, eeg, meg, electrocorticography, magnetic resonance, pet, spect, schema, metadata, neuroimaging, clinical neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Human Imaging Database |
PMID:21479735 | Free, Available for download, Freely available | nlx_155974 | http://www.xcede.org/XCEDE.html, http://www.nitrc.org/projects/qa_procedure, http://www.nitrc.org/projects/xcede | SCR_002571 | XML-Based Clinical Experiment Data Exchange Schema | 2026-09-19 12:50:01 | 2 | |||||
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pyxnat Resource Report Resource Website 1+ mentions |
pyxnat (RRID:SCR_002574) | pyxnat | software library, software resource, software toolkit | Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. | computed tomography, magnetic resonance, pet, spect, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
European Union | PMID:22654752 | Free, Available for download, Freely available | nlx_155977 | https://sources.debian.org/src/python-pyxnat/ | SCR_002574 | pyxnat: XNAT in Python | 2026-09-19 12:50:01 | 1 | ||||
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Presentation Resource Report Resource Website 1000+ mentions |
Presentation (RRID:SCR_002521) | Presentation | data analysis software, data processing software, software application, software resource | 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. | stimulus delivery, event logging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download | nlx_155925 | http://www.nitrc.org/projects/presentation | SCR_002521 | Presentation 19.0 | 2026-09-19 12:50:00 | 1570 | ||||||
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ParaView Resource Report Resource Website 500+ mentions |
ParaView (RRID:SCR_002516) | ParaView | data analysis software, data processing software, data visualization software, software application, software resource | Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data. | magnetic resonance |
uses: VTK is used by: Spine Detection and Extraction is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SIGEN has parent organization: Kitware |
Free, Available for download, Freely available | nlx_155917 | http://www.nitrc.org/projects/paraview, https://sources.debian.org/src/paraview/ | SCR_002516 | 2026-09-19 12:50:00 | 685 | |||||||
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Stochastic Tractography System Resource Report Resource Website |
Stochastic Tractography System (RRID:SCR_002594) | Stochastic Tractography System | data processing software, image analysis software, image processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images. | algorithm, reusable library, c++, linux, magnetic resonance, os independent, posix/unix-like, stochastic tractography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155998 | SCR_002594 | 2026-09-19 12:50:01 | 0 | ||||||||
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Spatial Statistical Parametric Mapping Resource Report Resource Website 1+ mentions |
Spatial Statistical Parametric Mapping (RRID:SCR_002592) | SSPM | data processing software, image analysis software, image processing software, software application, software resource | Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies. | imaging genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: Functional Analysis of Diffusion Tensor |
Free, Available for download, Freely available | nlx_155996 | SCR_002592 | 2026-09-19 12:50:01 | 1 | ||||||||
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ORS Visual SI Resource Report Resource Website 1+ mentions |
ORS Visual SI (RRID:SCR_002509) | ORS Visual SI | commercial organization, data processing software, data visualization software, software application, software resource | Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities. | active contour, animation, clipping, computed tomography, image display, image reconstruction, magnetic resonance, optical imaging, pet, spect, quantification, quantitative shape analysis, region growing, region of interest, rendering, segmentation, shape analysis, surface analysis, surface rendering, three dimensional display, two dimensional display, visualization, vitual endoscopy, volume measurement, volume rendering, volumetric analysis, english, french, italian, japanese, portuguese, spanish | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155908 | http://www.nitrc.org/projects/orsvisual_si | SCR_002509 | Object Research Systems Visual SI | 2026-09-19 12:49:59 | 1 | ||||||
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Normative Independent Component Analysis Resource Report Resource Website 1+ mentions |
Normative Independent Component Analysis (RRID:SCR_002506) | NICA | data analysis software, data processing software, software application, software resource | 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. | eeg, meg, electrocorticography, fourier time-domain analysis, independent component analysis, spectral analysis, statistical operation, temporal transformation, blind source separation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20598764 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155906 | http://www.nitrc.org/projects/nica | SCR_002506 | 2026-09-19 12:49:59 | 5 | ||||||
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Mouse BIRN Atlasing Toolkit Resource Report Resource Website 1+ mentions |
Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) | MBAT | data processing software, data visualization software, image analysis software, software application, software resource | Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels. | gene expression, microarray, light microscopy, electron microscopy, mri imaging, analyze, gnome, java, kde, magnetic resonance, nifti, os independent, win32 (ms windows), mri, registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse Biomedical Informatics Research Network is related to: 3D MRI Atlas of Mouse Development has parent organization: Laboratory of Neuro Imaging |
NCRR U24 RR021760 | PMID:21176225 | Free, Freely available, Available for download | nif-0000-00039 | http://mbat.loni.ucla.edu/ | SCR_002814 | MouseBIRN Atlasing Toolkit | 2026-09-19 12:50:09 | 2 | ||||
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NUTMEG Resource Report Resource Website 10+ mentions |
NUTMEG (RRID:SCR_002748) | NUTMEG | 1d time-series analysis software, data analysis software, data processing software, image analysis software, signal processing software, software application, software resource, time-series analysis software | 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. | MEG, EEG, analysis, reconstructing, neural, activation, overlaying, structural, MR, image, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at San Francisco; California; USA |
NIBIB EB022717; NIDCD F31 DC006762; NIDCD R01 DC004855 |
PMID:16012626 | nif-0000-24052 | http://www.nitrc.org/projects/nutmeg, | http://www.radiology.ucsf.edu/research/labs/biomagnetic-imaging/nutmeg | SCR_002748 | Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography | 2026-09-19 12:50:04 | 31 | ||||
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MIView Resource Report Resource Website |
MIView (RRID:SCR_000413) | MIView | data analysis software, data processing software, data visualization software, image processing software, software application, software resource | OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images. | medical image viewer, DICOM anonymizer, format conversion, read DICOM, analyze Nifti, raster images, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155661 | SCR_000413 | 2026-09-19 12:49:22 | 0 |
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