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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UNC Human Brain Atlas Resource Report Resource Website 1+ mentions |
UNC Human Brain Atlas (RRID:SCR_002606) | UNC Human Brain Atlas | reference atlas, data or information resource, atlas | Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes. | atlas data, magnetic resonance, nrrd, adult human, young human, pediatric, infant, late adult human, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center is related to: NeoSegPipeline has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Creative Commons Attribution-NonCommercial-ShareAlike License | nlx_156009 | SCR_002606 | 2025-04-03 11:01:50 | 3 | ||||||||
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ASL data processing tool box Resource Report Resource Website 1+ mentions |
ASL data processing tool box (RRID:SCR_005997) | software toolkit, software resource, data processing software, software application | Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis. | quantification, statistical operation, spm, arterial spin label, perfusion, mri, matlab, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: ASL spm8 has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
GNU General Public License | nlx_151371 | SCR_005997 | 2025-04-03 11:04:52 | 3 | |||||||||
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LONI Inspector Resource Report Resource Website 1+ mentions |
LONI Inspector (RRID:SCR_004923) | LONI Inspector | data processing software, software resource, software application | 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 | 2025-04-03 11:03:47 | 3 | |||||
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Functional Analysis of Diffusion Tensor Resource Report Resource Website 1+ mentions |
Functional Analysis of Diffusion Tensor (RRID:SCR_008888) | FADTTS | data processing software, software resource, software application | Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands. | genomic analysis, diffusion tensor imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Spatial Statistical Parametric Mapping |
Academic Free License | nlx_151351 | SCR_008888 | Functional Analysis of Diffusion Tensor Tract Statistics | 2025-04-03 11:07:58 | 3 | |||||||
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BrainVoyager Resource Report Resource Website 100+ mentions |
BrainVoyager (RRID:SCR_013057) | data processing software, software resource, software application, image analysis software | Commercial neuroimaging software package for multi-modal data analysis and management. It has been programmed in C++ with efficient statistical, numerical, and image processing routines. It supports parallelized basic math routines on all platforms and uses modern multi-core, multi-processor hardware for demanding computational routines. | image analysis, neuroimaging, software, multi modal data, data analysis, data management, fmri, eeg, dti, meg |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is affiliated with: Turbo-BrainVoyager is related to: BrainVoyager Brain Tutor is related to: BVQXtools is related to: NeuroElf has parent organization: Brain Innovation: Home of the BrainVoyager Product Family is parent organization of: BrainVoyager: Talairach Brain Atlas |
Commercial, License varies by geographic region | SCR_014267, nif-0000-00274 | SCR_013057 | BrainVoyager QX, Brain Voyager | 2025-04-03 11:09:42 | 171 | ||||||||
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Fiber Tracking Tool Resource Report Resource Website |
Fiber Tracking Tool (RRID:SCR_009474) | Fiber Tracking Tool | data processing software, software resource, software application, image analysis software | Used to analyze the fibers produced by ukf tractography | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155621 | SCR_009474 | 2025-04-03 11:08:17 | 0 | ||||||||
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Disease State Prediction Resource Report Resource Website |
Disease State Prediction (RRID:SCR_009467) | Disease State Prediction | data processing software, software resource, software application, image analysis software | These are the scripts used for the analyses reported in: Craddock RC, Holtzheimer PE, 3rd, Hu XP, Mayberg HS. (2009): Disease state prediction from resting state functional connectivity. Magn Reson Med 62(6):1619-28. Specifically included are scripts for performing t-test filter, reliability filter, recursive feature elimination, and reliability recursive feature elimination feature selection methods. These make use of wrappers that perform .632 bootstrap and k-fold cross validation strategies. The scripts are written in matlab and require the Bioinformatics toolbox. If you do not have the bioinformatics toolbox, the scripts can be easily modified to run with other matlab SVM toolboxes (i.e., libsvm, svmlight, shogun, etc.). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:19859933 | Creative Commons Attribution-NonCommercial License | nlx_155614 | SCR_009467 | 2025-04-03 11:08:17 | 0 | |||||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | data processing software, software resource, software application, image analysis software | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NIBIB EB025145; NIBIB R01 EB006385; NCRR P41 RR14075 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2 https://homer-fnirs.org/ |
SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2025-04-03 11:08:21 | 178 | ||||||
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IIT Human Brain Atlas Resource Report Resource Website 1+ mentions |
IIT Human Brain Atlas (RRID:SCR_009587) | IIT Human Brain Atlas | reference atlas, data or information resource, atlas | Atlas that contains new anatomical, DTI, HARDI templates and probabilistic gray matter labels of the adult human brain in ICBM-152 space. Artifact-free MRI data from 72 human subjects was used in the development of the atlas. All diffusion MRI data collection was conducted using Turboprop, and spatial normalization was accomplished in a population-based fashion. A description of the contents of the atlas can be found in the Downloads link. NOTE: The files of the older IIT2 DTI Brain Template are still available. However, the new DTI template of the IIT Human Brain Atlas (v.3) is of superior quality and allows more accurate registration across subjects. | atlas data, magnetic resonance, adult human, dti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Illinois Institute of Technology; Illinois; USA |
PMID:21218175 | Other/Commercial license License, Http://www.iit.edu/~mri/Downloads.html | nlx_155774 | http://www.nitrc.org/projects/iit | SCR_009587 | Illinois Institute of Technology Human Brain Atlas, The IIT Human Brain Atlas (v.3), IIT Human Brain Atlas (v.3) | 2025-04-03 11:08:21 | 7 | |||||
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HERMES Resource Report Resource Website 100+ mentions |
HERMES (RRID:SCR_009584) | HERMES | software toolkit, software resource, data processing software, software application | A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis. | clinical neuroinformatics, computational neuroscience, connectivity analysis, directed transfer analysis, eeg, meg, electrocorticography, granger causality, information theory, matlab, partial directed coherence, transfer entropy analysis, connectivity, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Polytechnic University of Madrid; Madrid; Spain |
Ministry of Education of the Community of Madrid NEUROTEU-CM program S2010/BMD-2460; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-01; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-03 |
GNU General Public License | nlx_155770 | http://www.nitrc.org/projects/hermes | SCR_009584 | HERramientas de MEdida de la Sincronizacion | 2025-04-03 11:08:21 | 131 | |||||
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DTI Fiber Tract Statistics Resource Report Resource Website 1+ mentions |
DTI Fiber Tract Statistics (RRID:SCR_009460) | DTI Fiber Tract Statistics | data processing software, software resource, software application, image analysis software | This is a command line tool which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts. Various tract-oriented scalar diffusion measures obtained from DTI brain images, are treated as a continuous function of white matter fibers'' arc-length. To analyze the trend along a given fiber tract, a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows (along the tract), such that they best represent the data and are robust to noise and Partial Volume effect. The package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions. The features available in the tool currently, its use and input / output formats and other relevant details are provided in the first draft of the documentation. (http://www.na-mic.org/Wiki/index.php/Projects:dtistatisticsfibers). | c, linux, magnetic resonance, posix/unix-like, regression, statistical operation, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155606 | SCR_009460 | 2025-04-03 11:08:17 | 3 | ||||||||
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INIA19 Primate Brain Atlas Resource Report Resource Website 1+ mentions |
INIA19 Primate Brain Atlas (RRID:SCR_009498) | INIA19 Primate Brain Atlas | reference atlas, data or information resource, atlas | Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas. | atlas data, magnetic resonance, nifti, neuromaps, brain atlas, mri, minimum-deformation template |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainInfo has parent organization: Integrative Neuroscience Initiative on Alcoholism |
PMID:23230398 | Creative Commons Attribution License | nlx_155646 | SCR_009498 | 2025-04-03 11:08:18 | 3 | |||||||
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Graphtools Resource Report Resource Website 1+ mentions |
Graphtools (RRID:SCR_009490) | Graphtools | data processing software, software resource, software application | A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user | magnetic resonance, matlab |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brain Connectivity Toolbox |
BSD License | nlx_155638 | SCR_009490 | 2025-04-03 11:08:18 | 4 | ||||||||
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resting-state pediatric imaging template Resource Report Resource Website |
resting-state pediatric imaging template (RRID:SCR_009647) | resting-state pediatric imaging template | reference atlas, data or information resource, atlas | Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates. | analyze, atlas data, magnetic resonance, child, resting-state, pediatric, adolescent | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public Domain | nlx_155978 | SCR_009647 | 2025-04-03 11:08:24 | 0 | ||||||||
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factory t1 dti Resource Report Resource Website |
factory t1 dti (RRID:SCR_009523) | factory_t1_dti | data processing software, software resource, software application, image analysis software | Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images. | magnetic resonance, analyze, t1, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155684 | SCR_009523 | factory t1 dti | 2025-04-03 11:08:19 | 0 | ||||||||
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GRETNA Resource Report Resource Website 100+ mentions |
GRETNA (RRID:SCR_009487) | GRETNA | data processing software, software resource, software application | A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field. | computational neuroscience, eeg, meg, electrocorticography, magnetic resonance, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: Functional Connectivity Analysis Tool for near-infrared spectroscopy data |
GNU General Public License | nlx_155634 | SCR_009487 | 2025-04-03 11:08:18 | 349 | ||||||||
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Generalized Covariance Analysis Resource Report Resource Website 1+ mentions |
Generalized Covariance Analysis (RRID:SCR_009488) | gCVA | data processing software, software resource, software application, image analysis software | A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.) | magnetic resonance, pet, spect, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155635 | SCR_009488 | Generalized Covariance Analysis (gCVA) | 2025-04-03 11:08:18 | 6 | |||||||
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GAMMA Resource Report Resource Website 500+ mentions |
GAMMA (RRID:SCR_009484) | GAMMA | data processing software, software resource, software application, image analysis software | GAMMA suite is an open-source cross-platform data mining software package designed to analyze neuroimaging data. A neuroimaging study often focuses on biomarker detection and classification. We designed and implemented a Bayesian, multivariate, nonparametric suite of algorithms for analyzing neuroimaging data. The GAMMA suite can be used for brain morphometric analysis, lesion-deficit analysis, and functional MR data analysis. | reusable library, analyze, c, c++, console (text based), computed tomography, cygwin, hp-ux, linux, macos, microsoft, modeling, magnetic resonance, nifti, pet, spect, posix/unix-like, quantification, statistical operation, volumetric analysis, win32 (ms windows), windows, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155632 | SCR_009484 | GAMMA Suite | 2025-04-03 11:08:18 | 559 | |||||||
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AutoSeg Resource Report Resource Website 10+ mentions |
AutoSeg (RRID:SCR_009438) | AutoSeg | data processing software, software resource, software application, image analysis software | A novel C++ based application developped at UNC-Chapel Hill that performs automatic brain tissue classification and structural segmentation. AutoSeg is designed for use with human and non-human primate pediatric, adolescent and adult data. AutoSeg uses a BatchMake pipeline script that includes the main steps of the framework entailing N4 bias field correction, rigid registration to a common coordinate image, tissue segmentation, skull-stripping, intensity rescaling, atlas-based registration, subcortical segmentation and lobar parcellation, regional cortical thickness and intensity statistics. AutoSeg allows efficient batch processing and grid computing to process large datasets and provides quality control visualizations via Slicer3 MRML scenes. | analyze, c++, expectation minimization, image-to-image, image-to-template, labeling, linux, macos, microsoft, magnetic resonance, nonlinear warp, nrrd, posix/unix-like, region of interest, registration, resampling, segmentation, spatial transformation, spline interpolation, volumetric analysis, warping, win32 (ms windows), windows, workflow, pediatric, adolescent, adult, young |
is used by: UNC-Wisconsin Neurodevelopment Rhesus MRI Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155582 | SCR_009438 | 2025-04-03 11:08:16 | 21 | ||||||||
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BXH/XCEDE Tools Resource Report Resource Website 1+ mentions |
BXH/XCEDE Tools (RRID:SCR_009439) | BXH/XCEDE Tools | data processing software, software resource, software application, image analysis 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 | 2025-04-03 11:08:16 | 4 |
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