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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
DIAMOND
 
Resource Report
Resource Website
1000+ mentions
DIAMOND (RRID:SCR_009457) DIAMOND software resource Software to: view dicom files and assemble them into 3D volumes. View and convert between Analyze, Nifti, and Interfile. Classify and organize dicoms and 3D volumes using metadata. Search and report on a collection of scans. reusable library, analyze, database application, dicom, format conversion, image display, image reconstruction, magnetic resonance, nifti, python, software, visualization, workflow, FASEB list is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of California at Davis; California; USA
nlx_155603 SCR_009457 UC Davis IDeA Lab Applications for Management Of Neuroimaging Data 2025-04-19 06:44:53 4052
NordicNeuroLab
 
Resource Report
Resource Website
10+ mentions
NordicNeuroLab (RRID:SCR_009632) NNL commercial organization From state of the art post-processing and visualization software for BOLD, Diffusion / DTI, and Perfusion / DCE imaging to fMRI hardware for audio and visual stimulation, eye tracking, and patient response collection, they provide products and solutions that define the field of functional MR imaging. They are dedicated to bringing the most advanced neuro-imaging tools to market while making functional MRI programs easy to implement. Through collaboration with research and clinical teams from both academic and medical centers, MR system manufacturers, and third party vendors they develop and manufacture hardware and software solutions that meet the needs of very experienced centers while developing training programs to make fMRI easy to adopt for more novice users. Their products are used around the world by researchers and clinicians alike. analyze, ascii, dicom, diffusion mr fiber tracking, experiment control, eye tracking, fiber tracking, haemodynamic response, hardware, microsoft, magnetic resonance, nifti, perfusion, physiological recording, scanner, stimulus presentation, temporal curve fitting, temporal transformation, tractography, windows, windows vista, windows xp, fmri, post-processing, visualization, bold, diffusion, dti, perfusion, dce, audio stimulation, visual stimulation, eye tracking, patient response, clinical, eye tracking device is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Commercial nlx_155905 http://www.nitrc.org/projects/nnl SCR_009632 2025-04-19 06:44:55 49
Brainsight
 
Resource Report
Resource Website
50+ mentions
Brainsight (RRID:SCR_009539) Brainsight resource, software resource Neuronavigation system for use in human cognitive neuroscience (TMS, EEG, NIRS) and for non-human neurosurgical applications. dicom, eeg, eeg, meg, electrocorticography, hardware, minc, minc2, magnetic resonance, nifti, nirs/fnir, optical imaging, optical imaging, philips par/rec, physiological recording, rendering, surface rendering, visualization, instrument, equipment is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Comercial Licence nlx_155718 http://www.nitrc.org/projects/brainsight SCR_009539 2025-05-02 11:01:28 53
pydicom
 
Resource Report
Resource Website
50+ mentions
pydicom (RRID:SCR_002573) pydicom software toolkit, software resource Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements. reusable library, console (text based), dicom, magnetic resonance, os independent, python is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
Free, Available for download, Freely available nlx_155976 http://www.nitrc.org/projects/pydicom
https://sources.debian.org/src/python3-pydicom/
http://pydicom.googlecode.com SCR_002573 2025-05-02 10:55:19 64
neurodebian
 
Resource Report
Resource Website
10+ mentions
neurodebian (RRID:SCR_004401) NeuroDebian data distribution software, software development tool, software development environment, source code, software repository, software resource, software application, data processing software Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note. linux, linux distribution, virtual machine, fmri, eeg, pymvpa, python, r, debian, brain image, neuroscience, platform, afni brik, bshort, bfloat, console (text based), dicom, domain independent, freebsd, gnome, kde, linux, minc2, nifti, philips par/rec, development environment, posix/unix-like, system administrator, web environment lists: MRIcron
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: ITK-SNAP
is related to: NITRC Computational Environment
is related to: PyMVPA
is related to: MRtrix
has parent organization: Debian
has parent organization: Dartmouth College; New Hampshire; USA
has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany
is parent organization of: VoxBo
is parent organization of: Computational Morphometry Toolkit
PMID:23055966 GNU General Public License v3, The community can contribute to this resource nlx_143723 http://www.nitrc.org/projects/neurodebian SCR_004401 Debian Neuroscience Repository, neuro debian 2025-05-05 11:05:09 36
1000 Functional Connectomes Project
 
Resource Report
Resource Website
10+ mentions
1000 Functional Connectomes Project (RRID:SCR_005361) INDI, 1000 FCP, FCP portal, image collection, data or information resource, project portal, image repository, database, data repository, storage service resource, service resource, catalog Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets. resting state functional mri, fmri, brain, neuroimaging, phenotype, function, data sharing, human, mri, r-fmri, rs-fmri, fc-fmri, rs--fcmri, resting-state, dicom, dti, child, adolescent, brain imaging, neuroinformatics, adult human, phenotype, data set, FASEB list is used by: NIF Data Federation
is used by: DataLad
is used by: Integrated Datasets
is used by: MetaSearch
is listed by: NITRC-IR
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: NIH Data Sharing Repositories
is affiliated with: Preprocessed Connectomes Project
is related to: Spanish Resting State Network
is related to: NITRC-IR
is related to: NIH Data Sharing Repositories
is related to: BASH4RfMRI
is related to: 1000 Functional Connectomes Project
has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC)
is parent organization of: C-PAC
is parent organization of: Neuro Bureau - Berlin Mind and Brain Sample
is parent organization of: Quiron-Valencia Sample
is parent organization of: ABIDE
is parent organization of: Consortium for Reliability and Reproducibility
is parent organization of: ADHD-200 Sample
is parent organization of: FCP Classic Data Sharing Samples
is parent organization of: NKI/Rockland Sample
is parent organization of: NYU Institute for Pediatric Neuroscience Sample
is parent organization of: Virginia Tech Carilion Research Institute Sample
is parent organization of: NKI-RS Multiband Imaging Test-Retest Pilot Dataset
is parent organization of: Beijing: Eyes Open Eyes Closed Study
is parent organization of: Beijing: Short TR Study
is parent organization of: COBRE
NITRIC PMID:23133413
PMID:23123682
Restricted SCR_015771, nlx_144428 http://www.nitrc.org/projects/fcon_1000/ SCR_005361 INDI, International Neuroimaging Data-Sharing Initiative, fcon_1000, Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI), 1000 Functional Connectomes Project, FCP/INDI 2025-05-05 11:05:56 46
Philips Users Community
 
Resource Report
Resource Website
1+ mentions
Philips Users Community (RRID:SCR_001438) Philips Users Community portal, data or information resource, community building portal Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know! community, dicom, magnetic resonance, nifti, philips par/rec is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) The community can contribute to this resource nlx_155922 SCR_001438 2025-05-05 11:02:17 1
NITRC Enhanced Services
 
Resource Report
Resource Website
NITRC Enhanced Services (RRID:SCR_002494) NITRC Enhanced Services portal, service resource, data or information resource, community building portal Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data. data, database, data resource, dicom, domain independent, information resource, nifti, platform or development environment, software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NITRC Computational Environment
is related to: NITRC-IR
has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC)
GNU General Public License nlx_155890 SCR_002494 2025-05-05 11:03:33 0
Slice:Drop
 
Resource Report
Resource Website
1+ mentions
Slice:Drop (RRID:SCR_002557) Slice:Drop analysis service resource, source code, production service resource, service resource, software resource 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 ). ascii, clinical neuroinformatics, computed tomography, dicom, javascript, mgh/mgz, magnetic resonance, nifti, nrrd, medical imaging, 3d, visualization, rendering is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) MIT License nlx_155964 http://www.nitrc.org/projects/slicedrop SCR_002557 2025-05-05 11:03:39 5
TractoR: Tractography with R
 
Resource Report
Resource Website
10+ mentions
TractoR: Tractography with R (RRID:SCR_002602) TractoR data visualization software, software resource, software application, data processing software 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. analyze, atlas application, c, dicom, linux, macos, modeling, magnetic resonance, nifti, other unix-like, posix/unix-like, quantification, r, segmentation, sh, bash, statistical operation, tractography, unix shell, visualization, diffusion mri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University College London; London; United Kingdom
GNU General Public License v2 nlx_156005 http://www.nitrc.org/projects/tractor SCR_002602 Tractography with R 2025-05-05 11:03:43 27
Template Image Processing Library
 
Resource Report
Resource Website
Template Image Processing Library (RRID:SCR_002600) TIPL image processing software, software library, software toolkit, image analysis software, software resource, software application, data processing software 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) reusable library, analyze, c++, dicom, format conversion, magnetic resonance, nifti, os independent, segmentation, spatial transformation, visualization, win32 (ms windows) is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Carnegie Mellon University; Pennsylvania; USA
BSD License nlx_156003 http://www.nitrc.org/projects/tipl SCR_002600 2025-05-05 11:03:43 0
TurtleSeg
 
Resource Report
Resource Website
1+ mentions
TurtleSeg (RRID:SCR_002605) TurtleSeg image analysis software, segmentation software, software resource, software application, data processing software 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. analyze, c++, computed tomography, dicom, intensity contour, microsoft, minc, magnetic resonance, nifti, segmentation, win32 (ms windows), windows, windows nt/2000, windows vista, windows xp is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) TurtleSeg License, Http://www.nitrc.org/include/glossary.php#594 nlx_156008 http://www.nitrc.org/projects/turtleseg SCR_002605 TurtleSeg - Interactive 3D Image Segmentation Software 2025-05-05 11:03:43 6
PANDA
 
Resource Report
Resource Website
100+ mentions
PANDA (RRID:SCR_002511) PANDA image processing software, workflow software, software toolkit, software resource, software application, data processing software A 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). analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Beijing Normal University; Beijing; China
National Natural Science Foundation of China ;
Beijing Nova Program ;
973 program ;
State Key Laboratory of Cognitive Neuroscience and Learning
PMID:23439846 GNU General Public License v3 nlx_155911 http://www.nitrc.org/projects/panda SCR_002511 PANDA: a pipeline tool for diffusion MRI, PANDA (Pipeline for Analyzing braiN Diffusion imAges), Pipeline for Analyzing braiN Diffusion imAges, PANDA: Pipeline for Analyzing braiN Diffusion imAges, panda-tool 2025-05-05 11:03:34 327
VoxBo
 
Resource Report
Resource Website
10+ mentions
VoxBo (RRID:SCR_002166) VoxBo image processing software, image analysis software, software resource, software application, data processing software Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more. fmri, neuroimaging, brain, functional, statistical, volume, preprocessing, analysis, display, format conversion, linear, three dimensional display, workflow, lesion, analyze, c++, console (text based), dicom, image display, linux, macos, microsoft, magnetic resonance, nifti, no input/output (daemon), overlap metrics, posix/unix-like, quantification, regression, resampling, sinc function interpolation, spatial transformation, statistical operation, visualization, windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: Debian
has parent organization: neurodebian
NIDA R01DA014418;
NIMH R01MH073529
PMID:22348882 Free, Available for download, Freely available nif-0000-00353 https://sources.debian.org/src/voxbo/
https://github.com/kimberg/voxbo
http://www.voxbo.org/ SCR_002166 2025-05-05 11:03:04 13
BRAINSFit
 
Resource Report
Resource Website
10+ mentions
BRAINSFit (RRID:SCR_002340) BRAINSFit software application, image analysis software, software resource, registration software, data processing software A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. 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 affine warp, analyze, c++, console (text based), dicom, image-to-image, intermodal, intersubject, linear warp, macos, microsoft, magnetic resonance, nifti, os independent, posix/unix-like, registration, spatial transformation, warping, windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) BSD License nlx_155701 http://www.nitrc.org/projects/multimodereg SCR_002340 2025-05-05 11:03:19 17
NeuroLens
 
Resource Report
Resource Website
1+ mentions
NeuroLens (RRID:SCR_007372) NeuroLens image processing software, data visualization software, image analysis software, software resource, software application, data processing software An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format image-to-image, linear, temporal convolution - deconvolution, multivariate analysis, neuroimaging, fmri, brain structure, neural structure, brain, temporal convolution, temporal deconvolution, afni brik, analyze, cor, dicom, image display, macos, mgh/mgz, minc, magnetic resonance, objective c, registration, regression, rendering, software, spatial transformation, statistical operation, surface rendering, temporal transformation, three dimensional display, visualization is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
has parent organization: University of Montreal; Quebec; Canada
MGH CSRL License, - free for academic and non-profit research use. nif-0000-00333 http://www.nitrc.org/projects/nldo SCR_007372 2025-05-05 11:07:48 8
MCIC
 
Resource Report
Resource Website
10+ mentions
MCIC (RRID:SCR_002310) MCIC data set, data or information resource Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data. clinical neuroinformatics, dicom, magnetic resonance, image collection, clinical assessment, diagnose, healthy control, neuropsychological test, psychiatric disorder, schizoaffective disorder, schizophrenia, diffusion-weighted is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Mind Research Network - COINS
Schizophrenia, Normal control PMID:23760817 COINS Data Use Agreement nlx_155657 SCR_002310 2025-05-05 11:03:16 30
LONI Inspector
 
Resource Report
Resource Website
1+ mentions
LONI Inspector (RRID:SCR_004923) LONI Inspector software resource, software application, data processing software A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI. analyze, 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_155785 http://www.nitrc.org/projects/inspector http://www.loni.ucla.edu/Software/LONI-Inspector SCR_004923 2025-05-05 11:05:45 3
BXH/XCEDE Tools
 
Resource Report
Resource Website
1+ mentions
BXH/XCEDE Tools (RRID:SCR_009439) BXH/XCEDE Tools image analysis software, software resource, software application, data processing software A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. analyze, c, c++, console (text based), dicom, format conversion, linux, macos, mgh/mgz, microsoft, minc, magnetic resonance, nifti, perl, posix/unix-like, quantification, sh/bash, statistical operation, unix shell, windows is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Function BIRN
BIRN License nlx_155583 SCR_009439 2025-05-05 11:09:48 4
DSI Studio
 
Resource Report
Resource Website
100+ mentions
DSI Studio (RRID:SCR_009557) DSI Studio image analysis software, software resource, software application, data processing software A software for diffusion MR images analysis. The provided functions include reconstruction (DTI, QBI, DSI, and GQI), deterministic fiber tracking, and 3D visualization. It has a window-based interface and operates on Microsoft Windows system. analyze, c++, console (text based), dicom, diffusion mr fiber tracking, diffusion spectrum, fiber tracking, image reconstruction, linux, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, q-ball, quantification, super tensor, tensor metric, tractography, visualization, win32 (ms windows), windows, coregistration, analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Carnegie Mellon University; Pennsylvania; USA
BSD License nlx_155737 http://www.nitrc.org/projects/dsistudio SCR_009557 2025-05-05 11:09:54 488

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