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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Functional Connectivity Community Resource Report Resource Website |
Functional Connectivity Community (RRID:SCR_009480) | Functional Connectivity Community | narrative resource, discussion, community building portal, data or information resource, portal | A community for the discussion of functional connectivity and all related topics. This includes discussion of related tools, data sets, methodological discussion, related websites and publications, etc. | community, knowledge environment, magnetic resonance, os independent, web environment, functional connectivity | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155627 | SCR_009480 | 2025-05-19 01:35:57 | 0 | |||||||||
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GIFTI Resource Report Resource Website 10+ mentions |
GIFTI (RRID:SCR_009579) | GIfTI | standard specification, software resource, data or information resource, narrative resource | Geometry format under the Neuroimaging Informatics Technology Initiative (NIfTI). Basically, it is the surface-file format complement to the NIfTI volume-file format .nii. Programs which support the Gifti format, intended to allow exchange of each others surface files, include: Freesurfer, Caret, BrainVISA, Brain Voyager, CRkit, VisTrails and AFNI. | algorithm or reusable library, c, computational neuroscience, information resource, magnetic resonance, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Neuroimaging Informatics Technology Initiative |
nlx_155761 | SCR_009579 | 2025-05-19 01:36:00 | 26 | |||||||||
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elastix Resource Report Resource Website 100+ mentions |
elastix (RRID:SCR_009619) | elastix | software application, software toolkit, registration software, data processing software, image analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023. Software toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. A paper describing elastix contains more details: S. Klein, M. Staring, K. Murphy, M.A. Viergever, J.P.W. Pluim, elastix: a toolbox for intensity based medical image registration,; IEEE Transactions on Medical Imaging, vol. 29, no. 1, pp. 196 - 205, January 2010. | reusable library, analyze, c++, console (text based), domain independent, nifti, nrrd, os independent, philips par/rec, registration, resampling, spatial transformation, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools is related to: Insight Segmentation and Registration Toolkit has parent organization: Utrecht University; Utrecht; Netherlands |
PMID:19923044 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155845, biotools:elastix | http://www.nitrc.org/projects/elastix https://bio.tools/elastix https://sources.debian.org/src/elastix/ |
SCR_009619 | 2025-05-19 01:36:01 | 162 | ||||||
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BrainBrowser Resource Report Resource Website 1+ mentions |
BrainBrowser (RRID:SCR_009535) | BrainBrowser | service resource, production service resource, data analysis service, data set, analysis service resource, data or information resource | A web-enabled brain surface viewer that allows the user to explore in real time a 3D brain map expressed on a base surface. BrainBrowser has two modes of operation, exploring either a pre-calculated database of structural correlation maps or working with user-defined data. In this mode, the user may choose to explore the correlation structure for cortical thickness, cortical area or cortical volume, or any other pre-calculated metric. In the second mode, the user is prompted for the local filenames of the statistical map and the base surface. BrainBrowser can also be used to manipulate 3D fibre pathways derived from DTI, using the same simple file format (.obj) as for surface data. BrainBrowser on Youtube: http://www.youtube.com/watch?v=HlRTUYUf1Ew NOTE: BrainBrowser requires a WebGL-enabled browser such as Google Chrome to support its 3D graphics capability. | image display, javascript, minc2, magnetic resonance, nifti, os independent, rendering, ruby, surface rendering, three dimensional display, two dimensional display, visualization, volume rendering, 3d visualization, neuroimaging, fmri, web application, web resource, data visualization service |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
Free | nlx_155710 | http://www.nitrc.org/projects/brainbrowser | SCR_009535 | 2025-05-19 01:35:59 | 3 | |||||||
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ADJUST Resource Report Resource Website 1000+ mentions |
ADJUST (RRID:SCR_009526) | ADJUST | software resource | A completely automatic algorithm for artifact identification and removal in EEG data. ADJUST is based on Independent Component Analysis (ICA), a successful but unsupervised method for isolating artifacts from EEG recordings. ADJUST identifies artifacted ICA components by combining stereotyped artifact-specific spatial and temporal features. Features are optimised to capture blinks, eye movements and generic discontinuities. Once artifacted IC are identified, they can be simply removed from the data while leaving the activity due to neural sources almost unaffected. | eeg, meg, electrocorticography, matlab, os independent |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institute of Health and Medical Research; Rennes; France |
PMID:20636297 | GNU General Public License | nlx_155689 | http://www.nitrc.org/projects/adjust | SCR_009526 | ADJUST - EEG Automatic Artifact Removal, ADJUST: automatic algorithm for EEG artifact removal | 2025-05-19 01:35:58 | 1437 | |||||
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SPM SS - fMRI functional localizers Resource Report Resource Website 1+ mentions |
SPM SS - fMRI functional localizers (RRID:SCR_009644) | spm_ss | software application, software toolkit, data processing software, image analysis software, software resource | Spm-toolbox that performs region of interest (ROI)-level and voxel-level between-subjects analyses of functional MRI data, restricting the analyses to those areas identified using subject-specific functional localizers. Methods: The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics) This toolbox requires Matlab and SPM5/SPM8. | analyze, linear, matlab, modeling, magnetic resonance, nifti, os independent, regression, statistical operation, win32 (ms windows), statistical parametric mapping, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
MIT License, X Consortium License | nlx_155955 | http://www.nitrc.org/projects/spm_ss | SCR_009644 | spm_ss toolbox, SPM toolbox for subject-specific analyses | 2025-05-19 01:36:02 | 5 | ||||||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | service resource, data set, data or information resource, storage service resource, data repository |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | Cerebral Blood Flow Biomedical Informatics Research Network | 2025-05-19 01:35:59 | 3 | ||||
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RapidArt Resource Report Resource Website |
RapidArt (RRID:SCR_000422) | RapidArt | software resource, software application, data analysis software, data processing software | 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, Available for download, Freely available | nlx_155941 | SCR_000422 | 2025-05-19 01:30:51 | 0 | ||||||||
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BrainFX Resource Report Resource Website |
BrainFX (RRID:SCR_000302) | BrainFX | software resource, software application, data processing software, 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) | Available for download | nlx_155712 | http://www.nitrc.org/projects/brainfx | http://www.brainfx.org/ | SCR_000302 | 2025-05-19 01:30:48 | 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 |
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 | 2025-05-19 01:31:00 | 2 | ||||||||
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JIST: Java Image Science Toolkit Resource Report Resource Website 10+ mentions |
JIST: Java Image Science Toolkit (RRID:SCR_008887) | JIST | software resource, software application, data processing software | A native Java-based imaging processing environment similar to the ITK/VTK paradigm. Initially developed as an extension to MIPAV (CIT, NIH, Bethesda, MD), the JIST processing infrastructure provides automated GUI generation for application plug-ins, graphical layout tools, and command line interfaces. This repository maintains the current multi-institutional JIST development tree and is recommended for public use and extension. JIST was originally developed at IACL and MedIC (Johns Hopkins University) and is now also supported by MASI (Vanderbilt University). | experimental control, modeling, quantification, segmentation, shape analysis, spatial transformation, workflow, macos, windows, os independent, bsd, linux, sunos/solaris, java, afni brik, analyze, cor, dicom, gifti, mgh/mgz, minc, minc2, nifti-1, nrrd, philips par/rec, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: Maps4Mipav (Exploratory JIST) is related to: MR Connectome Automated Pipeline is related to: Multi-Modal MRI Reproducibility Resource is related to: TOADS-CRUISE Brain Segmentation Tools is related to: CBS High-Res Brain Processing Tools is related to: JHU Proj. in Applied Medical Imaging is related to: DOTS WM tract segmentation has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Vanderbilt University; Tennessee; USA |
NINDS 5R01NS037747; NINDS 1R01NS056307; NIA N01-AG-4-0012 |
PMID:20077162 | GNU Lesser General Public License | nlx_151344 | https://sources.debian.org/src/jist/ | SCR_008887 | Java Image Science Toolkit | 2025-05-19 01:45:20 | 20 | ||||
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Neurophysiological Biomarker Toolbox Resource Report Resource Website 10+ mentions |
Neurophysiological Biomarker Toolbox (RRID:SCR_009612) | NBT | software application, software resource, data processing software, software toolkit | An open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT offers a pipeline from data storage to statistics including artifact rejection, signal visualization, biomarker computation, and statistical testing. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki that facilitates collaboration among NBT users including extensive help and tutorials. NBT is specialized in analyzing EEG data, however it allows the processing of any kind of signal. NBT can, e.g., be used to analyze ongoing oscillation between: * Eyes-closed rest of subject populations (e.g., healthy subjects and patients, males vs. females, young vs. old, etc.). * Two experimental condition (e.g., classical eyes-closed rest vs. meditation, or before vs. after consumption of a CNS-active substance (a drug, coffee, nicotine, alcohol, etc.). | brain vision analyzer data exchange format, database application, edf/bdf/gdf, eeg format, eeg, meg, electrocorticography, egi, fourier time-domain analysis, matlab, os independent, statistical operation, temporal transformation, temporal wavelet analysis, visualization, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: VU University; Amsterdam; Netherlands |
GNU General Public License | nlx_155831 | http://www.nitrc.org/projects/nbt | SCR_009612 | The Neurophysiological Biomarker Toolbox | 2025-05-19 01:45:24 | 32 | ||||||
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MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | software application, software resource, data processing software, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2025-05-19 01:45:24 | 1242 | ||||||
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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 | software resource, software application, data processing software | 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 | 2025-05-19 01:45:23 | 1 | |||||||
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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 | training resource, workshop, 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 | 2025-05-19 01:43:14 | 0 | |||||||
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NiLearn Resource Report Resource Website 100+ mentions |
NiLearn (RRID:SCR_001362) | NiLearn | software application, software toolkit, image processing software, software library, data processing software, software resource | A software package to facilitate the use of statistical learning on NeuroImaging data. Namely NiLearn leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis. | analyze, clinical neuroinformatics, magnetic resonance, nifti, os independent, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
Available for download | nlx_155897 | http://www.nitrc.org/projects/nilearn | SCR_001362 | NiLearn: Machine learning for Neuro-Imaging in Python | 2025-05-19 01:43:12 | 309 | ||||||
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FMRISTAT - A general statistical analysis for fMRI data Resource Report Resource Website 1+ mentions |
FMRISTAT - A general statistical analysis for fMRI data (RRID:SCR_001830) | FMRISTAT | software resource, software application, data processing software, image analysis software | A Matlab toolbox for the statistical analysis of fMRI data. The fMRI data was first converted to percentage of whole volume. The statistical analysis of the percentages was based on a linear model with correlated errors. The design matrix of the linear model was first convolved with a hemodynamic response function modelled as a difference of two gamma functions timed to coincide with the acquisition of each slice. Temporal drift was removed by adding a cubic spline in the frame times to the design matrix (one covariate per 2 minutes of scan time), and spatial drift was removed by adding a covariate in the whole volume average. The correlation structure was modelled as an autoregressive process of degree 1. At each voxel, the autocorrelation parameter was estimated from the least squares residuals using the Yule-Walker equations, after a bias correction for correlations induced by the linear model. The autocorrelation parameter was first regularized by spatial smoothing, then used to "whiten" the data and the design matrix. The linear model was then re-estimated using least squares on the whitened data to produce estimates of effects and their standard errors. In a second step, runs, sessions and subjects were combined using a mixed effects linear model for the effects (as data) with fixed effects standard deviations taken from the previous analysis. This was fitted using ReML implemented by the EM algorithm. A random effects analysis was performed by first estimating the the ratio of the random effects variance to the fixed effects variance, then regularizing this ratio by spatial smoothing with a Gaussian filter. The variance of the effect was then estimated by the smoothed ratio multiplied by the fixed effects variance. The amount of smoothing was chosen to achieve 100 effective degrees of freedom. The resulting T statistic images were thresholded using the minimum given by a Bonferroni correction and random field theory, taking into account the non-isotropic spatial correlation of the errors. | fmri, pet, statistical analysis, afni brik, analyze, console (text based), linear, matlab, minc, modeling, magnetic resonance, nifti, os independent, principal component analysis, regression, statistical operation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: McGill University; Montreal; Canada |
PMID:11771969 | Free | nif-0000-00303 | http://www.nitrc.org/projects/fmristat | http://www.bic.mni.mcgill.ca/users/keith/ | SCR_001830 | 2025-05-19 01:44:55 | 2 | |||||
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Quantitative Diffusion Tools Resource Report Resource Website |
Quantitative Diffusion Tools (RRID:SCR_002527) | Quantitative Diffusion Tools | software resource, software application, data processing software | Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc. | c++, magnetic resonance, os independent, quantification, segmentation, tractography | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | 3D Slicer License | nlx_155933 | SCR_002527 | 2025-05-19 01:44:57 | 0 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | software resource, software application, data processing software, image analysis software | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
MINC Licence, (BSD'ish), http://www.nitrc.org/include/glossary.php#527 | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2025-05-19 01:44:57 | 105 | ||||||
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LONI De-identification Debablet Resource Report Resource Website |
LONI De-identification Debablet (RRID:SCR_009593) | LONI De-identification Debablet | software resource, software application | 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 | 2025-05-19 01:49:43 | 0 |
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