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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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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CMFreg Resource Report Resource Website |
CMFreg (RRID:SCR_000171) | CMFreg | data processing software, image analysis software, registration software, software application, software resource | A sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a stable structure of reference can be used without the simple best fit of all surfaces. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155534 | SCR_000171 | 2026-09-19 12:49:17 | 0 | ||||||||
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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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RapidArt Resource Report Resource Website |
RapidArt (RRID:SCR_000422) | RapidArt | data analysis software, data processing software, software application, software resource | 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. | fMRI data analysis, detecting artifacts, individual region-of-interest based statistical analysis, nifti, os independent, python, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Artifact Detection Tools |
Free, Freely available | nlx_155941 | SCR_000422 | 2026-09-19 12:49:23 | 0 | ||||||||
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BrainFX Resource Report Resource Website |
BrainFX (RRID:SCR_000302) | BrainFX | data processing software, software application, software resource, workflow software | A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces. | java, magnetic resonance, nifti, os independent, development environment, software, workflow | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155712 | http://www.nitrc.org/projects/brainfx | http://www.brainfx.org/ | SCR_000302 | 2026-09-19 12:49:20 | 0 | ||||||
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NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH084358; NIMH R43 MH60507; NIMH R44 MH60507 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-09-19 12:49:26 | 0 | |||||||
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LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | data processing software, data visualization software, software application, software resource | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-09-19 12:49:29 | 0 | ||
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PyNIfTI Resource Report Resource Website 1+ mentions |
PyNIfTI (RRID:SCR_000693) | software resource | PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays. | reusable library, analyze, magnetic resonance, nifti, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NiBabel has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
Free, Available for download, Freely available | nlx_155929 | http://www.nitrc.org/projects/pynifti | SCR_000693 | PyNIfTI - Pythonic access to NIfTI and ANALYZE files, Pythonic access to NIfTI and ANALYZE files | 2026-09-19 12:49:28 | 2 | |||||||
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DicomBrowser Resource Report Resource Website 1+ mentions |
DicomBrowser (RRID:SCR_000864) | DicomBrowser | data processing software, image analysis software, software application, software resource, standalone software | A platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. DicomBrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation. | dicom, java, magnetic resonance, system administrators |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Washington University in St. Louis; Missouri; USA |
Free, Available for download, Freely available | nlx_155743 | http://www.nitrc.org/projects/dicom_browser | SCR_000864 | 2026-09-19 12:49:31 | 3 | |||||||
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imcalc: SPM batch image calculator Resource Report Resource Website 10+ mentions |
imcalc: SPM batch image calculator (RRID:SCR_000868) | imcalc | data processing software, image analysis software, software application, software resource, software toolkit | A collection of functions with batch functionality for SPM: * user entered expression (one set of volumes); * binarize non-zero voxels; * binarize/threshold each image; * binarize non-zero voxels, sum, rebinarize; * voxelwise calculations on pairs (add sub mult div ... etc.); * flip sign of all non-zero voxels; * x-flip image along y = 0; * mask images to a template; * T-to-Z transform; * Winsorize (cap) extreme values; * Z-score transform of image relative to its global mean and SD; * write single voxels to a .nii; * create a cluster image; * split cluster image into constituent images; * write hemisphere masks from template; * homotopic calculations; * replace zeros with __; * pad image with extra voxels; | magnetic resonance, statistical operation, batch functionality, spm |
is used by: SPM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National University of Singapore; Singapore; Singapore |
Free, Freely available | nlx_155854 | SCR_000868 | SPM batch image calculator, SPM batch image calculator (imcalc) | 2026-09-19 12:49:31 | 15 | |||||||
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OpenElectrophy Resource Report Resource Website 10+ mentions |
OpenElectrophy (RRID:SCR_000819) | OpenElectrophy | data analysis software, data processing software, software application, software resource | Software Python module for electrophysiology data analysis. | neurophysiology, electrophysiology, python, intracellular, extracellular, data sharing, analysis sharing, neural signal, spike, oscillation, mysql, eeg, meg, electrocorticography |
uses: Neo is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: NeuralEnsemble |
NIBIB 5R24EB029173 | PMID:19521545 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151873 | http://www.nitrc.org/projects/openelectrophy, https://sources.debian.org/src/openelectrophy/ | SCR_000819 | 2026-09-19 12:49:31 | 10 | |||||
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BRAINSCut Resource Report Resource Website |
BRAINSCut (RRID:SCR_000861) | BRAINSCut | data processing software, image analysis software, segmentation software, software application, software resource | A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: GitHub is listed by: INCF Software Center has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155699 | SCR_000861 | 2026-09-19 12:49:30 | 0 | ||||||||
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GesTr Resource Report Resource Website |
GesTr (RRID:SCR_000857) | GesTr | software resource | A cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device. | domain independent, gesture, tracking | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155637 | SCR_000857 | 2026-09-19 12:49:31 | 0 | ||||||||
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COMPARE Resource Report Resource Website 1+ mentions |
COMPARE (RRID:SCR_000855) | COMPARE | data processing software, image processing software, software application, software resource | Generic classification tool for 3D images | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155598 | SCR_000855 | 2026-09-19 12:49:30 | 1 | ||||||||
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Data Format Tools Resource Report Resource Website |
Data Format Tools (RRID:SCR_000856) | DFT | software resource | A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand. | console (text based), dicom, format conversion, macos, magnetic resonance, nifti, posix/unix-like, python, system administrators, visualization, web environment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155608 | SCR_000856 | 2026-09-19 12:49:30 | 0 |
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