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http://www.nitrc.org/projects/scribe/

Scribe encodes papers to populate the BrainMap Database

Proper citation: Scribe (RRID:SCR_000423) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ontologyviz/

Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.

Proper citation: Faceted Search Based Ontology Visualizer (RRID:SCR_000124) Copy   

•   Source: SciCrunch Registry

http://neurolex.org/wiki/Main_Page

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

Proper citation: NeuroLex (RRID:SCR_005402) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/xnat_extras

User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org

Proper citation: XNAT Extras (RRID:SCR_004759) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ccsegthickness

An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python.

Proper citation: Corpus Callosum Thickness Profile Analysis Pipeline (RRID:SCR_003575) Copy   

•   Source: SciCrunch Registry

http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

•   Source: SciCrunch Registry

https://osf.io/

Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.

Proper citation: Open Science Framework (RRID:SCR_003238) Copy   

•   Source: SciCrunch Registry

http://www.thevirtualbrain.org/

Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders.

Proper citation: Virtual brain (RRID:SCR_002249) Copy   

•   Source: SciCrunch Registry

http://wiki.biac.duke.edu/jvs:cigal

Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables).

Proper citation: CIGAL (RRID:SCR_002232) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/uncbcp_4d_atlas/

Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications.

Proper citation: 4D Atlases Construction (RRID:SCR_002227) Copy   

•   Source: SciCrunch Registry

http://omlc.ogi.edu/software/mc/

MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications.

Proper citation: MCML and CONV (RRID:SCR_002419) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/multi_t2/

Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches.

Proper citation: Multicomponent T2 estimation with stimulated echo correction (RRID:SCR_002446) Copy   

•   Source: SciCrunch Registry

http://neuronetrix.com/

A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).

Proper citation: COGNISION (RRID:SCR_002362) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ontology/

Project to discuss, debate, develop and deploy ontological practices for the fMRI community.

Proper citation: Resource Ontology Discussion Group (RRID:SCR_002536) Copy   

•   Source: SciCrunch Registry

http://nipy.org/nibabel/

A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.

Proper citation: NiBabel (RRID:SCR_002498) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/pythagoras/

Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment.

Proper citation: Pythagorean Displacement and Motion Regressors (RRID:SCR_002525) Copy   

•   Source: SciCrunch Registry

http://www.sdmproject.com/

Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera).

Proper citation: Signed Differential Mapping (RRID:SCR_002554) Copy   

•   Source: SciCrunch Registry

http://www.trianglebiosystems.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software

Proper citation: Triangle BioSystems (RRID:SCR_002603) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/tmma

An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left.

Proper citation: TetraMetrix (RRID:SCR_002601) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/penncnv

A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

Proper citation: PennCNV (RRID:SCR_002518) Copy   

•   Source: SciCrunch Registry