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https://github.com/BlueBrain/BluePyOpt
An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.
Proper citation: BluePyOpt (RRID:SCR_014753) Copy
http://www.nitrc.org/projects/vini/
Software Python tool as viewer for MRI data and numpy arrays.
Proper citation: vini: A viewer for fMRI data (RRID:SCR_017250) Copy
https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases
Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.
Proper citation: MeshView (RRID:SCR_017222) Copy
Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.
Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy
https://github.com/bheAI/MonkeyCBP_CLI
Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.
Proper citation: MonkeyCBP (RRID:SCR_017640) Copy
http://www.nitrc.org/projects/kwyk/
Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation.
Proper citation: Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) Copy
http://www.nitrc.org/projects/pennhippoatlas/
Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.
Proper citation: Penn Hippocampus Atlas (RRID:SCR_000421) Copy
http://www.nitrc.org/projects/licensing/
Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.
Proper citation: Licensing issues in software and data (RRID:SCR_000411) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU).
Proper citation: Kymata Atlas (RRID:SCR_000269) Copy
A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).
Proper citation: BraVa (RRID:SCR_001407) Copy
http://miriad.drc.ion.ucl.ac.uk/
A database of volumetric MRI brain-scans of 46 Alzheimer's sufferers and 23 healthy elderly people. Many scans were collected of each participant at intervals from 2 weeks to 2 years, the study was designed to investigate the feasibility of using MRI as an outcome measure for clinical trials of Alzheimer's treatments. It includes a total of 708 scans and should be of particular interest for work on longitudinal biomarkers and image analysis.
Proper citation: MIRIAD (RRID:SCR_002422) Copy
http://www.nitrc.org/projects/brainarteries/
Stereotactic atlases with probabilistic values describing the location of the main cerebral arteries. The data collected are from the COBRA study as described in "COBRA: A prospective multimodal imaging study of dopamine, brain structure and function, and cognition" by Nevalainen et al.
Proper citation: Umea Brain Arteries (RRID:SCR_014752) Copy
http://www.nitrc.org/projects/whs-sd-atlas/
Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.
Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy
http://www.nitrc.org/projects/reliability/
Data collected from subjects scanned 3 times (V1, V2, V3), with V1 and V2 on a scanner, V3 on another scanner in another site. Resting state blood oxygenation level dependent functional MRI (BOLD fMRI), pseudo continuous arterial spin labeling (pCASL), and high resolution 3D T1 imaging were performed under eyes open (EO) and eyes closed (EC) conditions.
Proper citation: Intra- and inter-scanner reliability of RS-fMRI BOLD and ASL with eyes closed vs. eyes open (RRID:SCR_016935) Copy
http://www.nitrc.org/projects/miitra/
Atlas for studies of older adult brain. Includes T1-weighted template of older adult brain and tissue probability maps. Exhibits high image sharpness, provides higher inter-subject spatial normalization accuracy compared to other standardized templates and similar normalization accuracy to well-constructed study-specific templates.
Proper citation: MIITRA atlas (RRID:SCR_017566) Copy
http://www.nitrc.org/projects/onprc18_atlas/
Atlas includes co-registered templates constructed from MR images frequently used to characterize macroscopic brain structure T2/SPACE and T1/MP-RAGE, and diffusion tensor imaging template.
Proper citation: ONPRC18 Multimodal MRI Atlas (RRID:SCR_019073) Copy
A software program for source imaging Magnetoencephalographic data. Now MEG tools has added Imaged Coherence mapping, Talairach and MNI coordinates, Grainger Causality. MEG Tools also includes MR-FOCUSS, ECD, Beamformers and many other useful MEG tools. This is a Matlab-based software module that is used to image MEG data onto a patient's MRI. This software imports all MEG manufacture's data (4D-Neuroimaging/BTi, CTF and Neuromag/Elekta).
Proper citation: MEG Tools (RRID:SCR_000661) Copy
http://www.loni.usc.edu/Software/Debabeler
Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM.
Proper citation: LONI Debabeler (RRID:SCR_001160) Copy
https://github.com/BRAINSia/BRAINSTools
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.
Proper citation: BRAINSCortex (RRID:SCR_001082) Copy
Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added.
Proper citation: INCF Software Center (RRID:SCR_002347) Copy
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