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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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g.BSanalyze Resource Report Resource Website 1+ mentions |
g.BSanalyze (RRID:SCR_009625) | g.BSanalyze | data processing software, software application, software resource | An interactive environment for multimodal biosignal data processing and analysis in the fields of clinical research and life sciences. It is the most comprehensive package to analyze non-invasive and invasive brain-, heart- and muscle-functions and dysfunctions. It includes many functions such as support vector machines, event-related ECG, support for P300 and SSVEP/SSSEP BCIs, zero class detection for BCIs, compressed spectral array, minimum energy, and more! g.BSanalyze consists of a base version for data import, visualization, transformation and pre-processing and has several dedicated toolboxes. The package comes with many sample biosignal data-sets, including P300, SSVEP, motor imagery, CSP BCIs, Tilt-Table, EPs, multi-unit activity, CFM, and ERD/ERS. | ascii, eeg, meg, matlab, microsoft, windows, clinical | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Other/Commercial license License | nlx_155850 | http://www.nitrc.org/projects/gbsanalyze | SCR_009625 | 2026-08-04 09:42:26 | 2 | |||||||
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HI-SPEED Software Packets Resource Report Resource Website 1+ mentions |
HI-SPEED Software Packets (RRID:SCR_009585) | HI-SPEED Software Packets | data processing software, software application, software resource | HI-SPEED Software Packets contain # unconstrained and constrained nonlinear least squares diffusion tensor estimation techniques, # 2-dimensional and 3-dimensional analytical (Shepp-Logan) magnetic resonance imaging phantoms in both the Fourier and image domains, # techniques for reporting the underlying signal-to-noise ratio in magnetic resonance (MR) images, # Probabilistic Identification and EStimation of NOise (PIESNO)---a technique for identifying noise-only pixels and estimating the underlying noise standard deviation in MR images, and # a signal-transformational technique for breaking the noise floor in MR images. Many more computational tools will be shared with users and developers as they become available. | reusable library, image reconstruction, java, modeling, magnetic resonance, os independent, statistical operation, tensor metric, mri, diffusion tensor mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
HI-SPEED Software Packets License | nlx_155771 | http://www.nitrc.org/projects/hispeed | SCR_009585 | 2026-08-04 09:42:24 | 1 | |||||||
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AMILab Resource Report Resource Website 1+ mentions |
AMILab (RRID:SCR_009525) | AMILab | data processing software, software application, software resource | An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK. | active contour, analyze, animation, artifact removal, bshort/bfloat, c++, dicom, domain independent, filtering, format conversion, fourier transform, frequency domain, gnome, image display, intensity contour, kde, linux, macos, medial axis, microsoft, minc, motion analysis, nrrd, posix/unix-like, python, quality metrics, rendering, resampling, segmentation, shape analysis, software, spatial transformation, spline interpolation, surface rendering, temporal transformation, two dimensional display, visualization, volume rendering, win32 (ms windows), windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:22356993 | GNU Lesser General Public License | nlx_155687 | http://www.nitrc.org/projects/amilab | SCR_009525 | 2026-08-04 09:42:24 | 1 | ||||||
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CURRY Resource Report Resource Website 100+ mentions |
CURRY (RRID:SCR_009546) | CURRY | data processing software, software application, software resource | Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package. | multimodal, atlas, application, connectivity, analysis, computed, tomography, database, eeg, meg, electrocorticography, modeling, finite, element, format, conversion, forward, inverse, image, reconstruction, meg, mesh, generation, model, magnetic resonance, pet, spect, segmentation, simulation, spatial, transformation, volumetric, neuroimaging, FASEB list | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155726 | http://www.nitrc.org/projects/curry_7 | SCR_009546 | CURRY Scan 7 Neuroimaging Suite, CURRY 8, CURRY 7, CURRY Neuroimaging Suite | 2026-08-04 09:42:24 | 160 | ||||||
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DTI Atlas Builder Resource Report Resource Website 1+ mentions |
DTI Atlas Builder (RRID:SCR_013112) | DTIAtlasBuilder | data processing software, software application, software resource | This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed. | magnetic resonance, dti, atlas | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155738 | http://www.nitrc.org/projects/dtiatlasbuilder | SCR_013112 | 2026-08-04 09:43:08 | 2 | |||||||
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Region to Region Resource Report Resource Website 1+ mentions |
Region to Region (RRID:SCR_016995) | data processing software, software application, software resource | Software tool as a framework for fitting and describing connectivity patterns between regions that is a simple extension from the current population receptive field models in the visual neuroscience literature. The connectivity from each voxel in a designated seed region to a mapping region is modeled as a 3-dimensional Gaussian, providing location parameters and spread parameters. This allows the direct description of the relative mapping from one region to another. | connectivity, pattern, region, neuroinformatics, region, receptive, field, model, visual, neuroscience, voxel, mapping, 3D, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Stony Brook University; New York; USA |
Free, Available for download, Freely available | SCR_016995 | 3-D Connective Field Modeling Toolbox | 2026-08-04 09:44:04 | 1 | |||||||||
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HeuDiConv: a heuristic-centric DICOM converter Resource Report Resource Website 10+ mentions |
HeuDiConv: a heuristic-centric DICOM converter (RRID:SCR_017427) | HeuDiConv | data processing software, software application, software resource | Software tool as flexible DICOM converter for organizing brain imaging data into structured directory layouts. | Flexible, DICOM, converter, organizing, brain, image, data, structured, directory, layout | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | http://www.nitrc.org/projects/heudiconv/ | SCR_017427 | heudiconv, heuristic-centric DICOM converter | 2026-08-04 09:44:13 | 28 | ||||||||
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NITRC Community Conferences Workshops and Meetings Resource Report Resource Website |
NITRC Community Conferences Workshops and Meetings (RRID:SCR_002323) | Conferences Workshops and Meetings | workshop, training resource, meeting resource | Project to assist the community in the support of information about upcoming Conferences, Workshops and Meetings. Such support may be documents, news, files, etc. To see a listing of upcoming Events, please use the NITRC Community Events Page at http://www.nitrc.org/incf/event_list.php (and tab at right). To announce an Event, please use the Submit an Event at the NITRC Community Events Page, http://www.incf.org/Events/events/createObject?type_name=Event (and tab at right). Note, INCF account is currently required. All users are encouraged to check this site for upcoming meetings, and promote future meetings here. | knowledge environment, os independent, conference, neuroinformatics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
The community can contribute to this resource, Account required | nlx_155672 | SCR_002323 | NITRC / INCF Community Conferences Workshops and Meetings | 2026-08-04 09:40:36 | 0 | |||||||
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DICOM UploadGUI Resource Report Resource Website |
DICOM UploadGUI (RRID:SCR_009458) | DICOM_UploadGUI | software application, software resource | A Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155604 | SCR_009458 | DICOM UploadGUI | 2026-08-04 09:42:23 | 0 | ||||||||
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FMRIpower Resource Report Resource Website 10+ mentions |
FMRIpower (RRID:SCR_009576) | fmripower | software application, software resource | An easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data. | analyze, linear, matlab, magnetic resonance, nifti, regression, statistical operation, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA |
PMID:17919925 | Public Domain | nlx_155757 | http://www.nitrc.org/projects/fmripower | SCR_009576 | 2026-08-04 09:42:24 | 16 | ||||||
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EEProbe Resource Report Resource Website 10+ mentions |
EEProbe (RRID:SCR_009570) | eeprobe | software application, software resource | A complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser. ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X. | eeg, meg, electrocorticography, event related potential, time domain analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155750 | http://www.nitrc.org/projects/eeprobe | SCR_009570 | 2026-08-04 09:42:24 | 26 | |||||||
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E-Prime Extensions for fMRI Resource Report Resource Website |
E-Prime Extensions for fMRI (RRID:SCR_009568) | EEfMRI | software application, software resource | Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime. | experimental control, microsoft, magnetic resonance, win32 (ms windows), windows, windows vista, windows xp, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Other/Commercial license License | nlx_155748 | http://www.nitrc.org/projects/eefmri | SCR_009568 | 2026-08-04 09:42:25 | 0 | |||||||
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Finsler tractography module for Slicer Resource Report Resource Website |
Finsler tractography module for Slicer (RRID:SCR_009477) | Finsler tractography module for Slicer | software application, software resource | This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required). The software can be built as either a stand-alone or a CLI plugin for 3D Slicer. | c++, connectivity analysis, console (text based), diffusion mr fiber tracking, diffusion spectrum, direction, fiber tracking, linux, macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, q-ball, super tensor, tensor metric, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer is parent organization of: Fiber-tracking based on Finsler distance |
3D Slicer License | nlx_155624 | SCR_009477 | 2026-08-04 09:42:24 | 0 | ||||||||
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LONI De-identification Debablet Resource Report Resource Website |
LONI De-identification Debablet (RRID:SCR_009593) | LONI De-identification Debablet | software application, software resource | Software application for removing patient-identifying information from medical image files. Removing this information is often necessary for enabling investigators to share image files in a HIPAA compliant manner. | analyze, console (text based), dicom, java, minc, magnetic resonance, nifti, os independent, win32 (ms windows), workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
LONI Software License | nlx_155784 | http://www.nitrc.org/projects/did | http://www.loni.ucla.edu/Software/Software_Detail.jsp?software_id=23 | SCR_009593 | 2026-08-04 09:42:24 | 0 | |||||
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BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-08-04 09:42:23 | 3 | |||||
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BESA Resource Report Resource Website 100+ mentions |
BESA (RRID:SCR_009530) | BESA | software application, software resource | Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI. | application, connectivity analysis, eeg, meg, electrocorticography, eeg modeling, event related potential, finite element analysis, forward - inverse, fourier time-domain analysis, independent component analysis, meg modeling, modeling, principal component analysis, source separation analysis, spectral analysis, statistical operation, surrogate data analysis, temporal transformation, time domain analysis, evoked potential, evoked field, event-related field, neuroimaging, mri, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155695 | http://www.nitrc.org/projects/besa | SCR_009530 | Brain Electrical Source Analysis | 2026-08-04 09:42:25 | 233 | ||||||
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Hitachi2nirs Resource Report Resource Website |
Hitachi2nirs (RRID:SCR_009494) | Hitachi2nirs | software application, software resource | A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file. | hardware, matlab, nirs, fnir, optical imaging, optical imaging, physiological recording | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155642 | SCR_009494 | 2026-08-04 09:42:24 | 0 | ||||||||
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ALVIN Resource Report Resource Website 1+ mentions |
ALVIN (RRID:SCR_009527) | ALVIN | software application, software resource | A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject. | magnetic resonance, quantification, region of interest, segmentation, software, volume measurement, volumetric analysis, volumetric analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155690 | http://www.nitrc.org/projects/alvin_lv | SCR_009527 | ALVIN - Automatic Lateral Ventricle delIneatioN, Automatic Lateral Ventricle delIneatioN, ALVIN - Lateral Ventricle Segmentation | 2026-08-04 09:42:24 | 6 | ||||||
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fMRI-CPCA Resource Report Resource Website 1+ mentions |
fMRI-CPCA (RRID:SCR_009520) | fMRI-CPCA, fMRI CPCA | software application, software resource | Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated. | analyze, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, principal component analysis, regression, statistical operation, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155682 | SCR_009520 | fMRI-Constrained Principal Component Analysis, fMRI Constrained Principal Component Analysis | 2026-08-04 09:42:24 | 7 | |||||||
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GAMBIT Resource Report Resource Website 50+ mentions |
GAMBIT (RRID:SCR_009483) | GAMBIT | software application, software resource | 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. | analyze, c++, linux, mesh generation, modeling, magnetic resonance, nrrd, posix/unix-like, surface analysis, thickness, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155631 | SCR_009483 | 2026-08-04 09:42:24 | 57 |
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