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

High quality data, open and freely available to everyone to celebrate the diversity of the vertebrate brain. Do you have data that you would like to share? Do not hesitate to contact them! The Brain Catalogue is developed by Florencia Grisanti (Taxidermy Workshop of the Natural History Museum in Paris) and Roberto Toro (Neuroscience Department of the Institut Pasteur). Many of our specimens come from the Vertebrate Brain Collection of the Jardin des Plantes, curated by Marc Herbin, and are scanned at the Institut du Cerveau et de la Moelle (ICM) by Mathieu Santin and Alexandra Petiet, from the CENIR laboratory, with financial and methodological support kindly provided by Olivier Colliot, head of the Cogimage team at the ICM.

Proper citation: Brain Catalogue (RRID:SCR_009442) Copy   

•   Source: SciCrunch Registry

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

3D DTI anatomical rat brain atlases have been created by the UNC- Chapel Hill Department of Psychiatry and the CAMID research collaboration. There are three age groups, postnatal day 5, postnatal day 14, and postnatal day 72. The subjects were Sprague-Dawley rats that were controls in a study on cocaine abuse and development. The P5 and P14 templates were made from scans of twenty rats each (ten female, ten male); the P72, from six females. The individual cases have been resampled to isotropic resolution, manually skull-stripped, and deformably registered via an unbiased atlas building method to create a template for each age group. Each template was then manually segmented using itk-SNAP software. Each atlas is made up of 3 files, a template image, a segmentation, and a label file.

Proper citation: 3D DTI Atlas of the Rat Brain In Postnatal Day 5 14 and Adulthood (RRID:SCR_009437) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://kymata-atlas.org

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   

•   Source: SciCrunch Registry

http://physics.ucsd.edu/neurophysics/links.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities.

Proper citation: MPScope (RRID:SCR_000065) Copy   

•   Source: SciCrunch Registry

http://www.psychopy.org

Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime.

Proper citation: PsychoPy (RRID:SCR_006571) Copy   

•   Source: SciCrunch Registry

http://www.uzh.ch/keyinst/loreta

Software package for functional imaging of human brain. Used to compute three dimensional distribution of electric neuronal activity from non-invasive measurements of scalp electric potential differences with high time resolution in millisecond range. Non-invasive intracranial time series are used for studying functional dynamic connectivity.. Current software version includes two new, improved variants of the original method: standardized (sLORETA) and exact (eLORETA). The new methods are characterized by exact localization when tested with point sources. Due to the fact that these methods are multivariate tomographies that are solutions to the inverse EEG problem, and that they are linear in nature, they will produce a low spatial resolution image for any distribution of activity. This property is not shared by naive one-at-a-time single dipole techniques.

Proper citation: Low Resolution Electromagnetic Tomography (RRID:SCR_007077) Copy   

•   Source: SciCrunch Registry

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

A Java tool that takes an unorganized collection of DICOM scans, sorts and categorizes them according to user-customizable rules, gathers metadata about the scans, and saves out this information to help facilitate data uploads. Batch pr

Proper citation: DICOM UploadGUI (RRID:SCR_009458) Copy   

•   Source: SciCrunch Registry

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

This package is a set of three slicer modules which together are able to compute a DWI Atlas given a set of DWI''s. The modules included are: # A Groupwise Registration module -> compute''s a deformation field for each DWI, using, for example, FA maps as input # Warp DWI module -> used to warp each DWI using the deformation from (1) # DWI Averager -> used to average the set of warped DWI''s producing the final DWI Atlas

Proper citation: Create DWI Atlas (RRID:SCR_009455) Copy   

•   Source: SciCrunch Registry

http://fmripower.org

An easy to use matlab-based graphical user interface that calculates power for future studies based on older analyses or pilot data.

Proper citation: FMRIpower (RRID:SCR_009576) Copy   

•   Source: SciCrunch Registry

http://www.ant-neuro.com/products/eeprobe

A complete software package for the study of event-related brain activity with high-resolution EEG/MEG. This package has been designed to suit the high standards of neuroscience research. The software has been developed originally at the Max Planck Institute for Cognitive Neuroscience in Leipzig, Germany, and is available for other institutions through ANT Neuro B.V., The Netherlands, enhanced with the EEProbe Databrowser. ERP investigations, both in psychophysiology research and clinical applications require a multitude of processing steps. Analysis of large data sets is made efficient through advanced scripting possibilities. All different aspects of data handling are efficiently available in the EEProbe Databrowser. Alternatively, external data can be imported from a multitude of formats. Processing in EEProbe makes use of open file formats (see LIBEEP) and is designed to integrate with ASA for advanced source analysis. EEProbe is available for Linux and Mac OS X.

Proper citation: EEProbe (RRID:SCR_009570) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/software.cfm?ID=101

Software designed to optimize E-Prime experiments for fMRI research. EEfMRI allows you to synchronize the start of your experiment with the first scanner trigger pulse along with several valuable features to enhance the control you have over your experiment. Implementing EEfMRI into your current experiments is achieved by simply dragging and dropping the correct EEfMRI package calls into the E-Prime experiment in the appropriate places. EEfMRI is designed to integrate with other PST hardware and software to increase usability for researchers while maintaining the millisecond accuracy of E-Prime.

Proper citation: E-Prime Extensions for fMRI (RRID:SCR_009568) Copy   

•   Source: SciCrunch Registry

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

A Matlab toolbox that allows computation of task-related functional connectivity between multiple pairs of regions. Task-related functional connectivity is computed using the correlational psychophysiological interaction (cPPI) methodology described in Fornito et al. (2012) PNAS, 109: 12788-12793. The toolbox assumes that first-level design matrices have been specified and estimated using SPM5 or later. It takes as input these design matrices as well as user-extracted regional time courses and returns a matrix of pair-wise, task-related functional connectivity for each participant. The method is scalable to large networks comprising hundreds of regions and is well-suited to graph theoretic analyses and functional connectomics. One modifiable script, cPPI_master.m, can be used to run the analysis for an entire sample of participants.

Proper citation: cPPI Toolbox for fMRI (RRID:SCR_009518) Copy   

•   Source: SciCrunch Registry

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

This module implements the Finsler tractography method with HARDI data described by J. Melonakos et al. From a set of seeding and target points, the paths are estimated as the shortest path taking into account a local, directional dependent cost. The output provided is the connectivity map from each voxel in the volume to the seeding points, plus a vector volume with the directions tangent to the fiber bundles at each point. If the Backtracing module within is built, these directions can be traced back to actually compute the fiber bundles (VTK required). The software can be built as either a stand-alone or a CLI plugin for 3D Slicer.

Proper citation: Finsler tractography module for Slicer (RRID:SCR_009477) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/DiD

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.

Proper citation: LONI De-identification Debablet (RRID:SCR_009593) Copy   

•   Source: SciCrunch Registry

http://www.sci.utah.edu/cibc/software/231-biomesh3d.html

A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.

Proper citation: BioMesh3D (RRID:SCR_009534) Copy   

•   Source: SciCrunch Registry

http://besa.de

Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI.

Proper citation: BESA (RRID:SCR_009530) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hitachi2nirs/

A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file.

Proper citation: Hitachi2nirs (RRID:SCR_009494) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gig-ica/

Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too.

Proper citation: Group Information Guided ICA (RRID:SCR_009491) Copy   

•   Source: SciCrunch Registry

http://sites.google.com/site/mrilateralventricle/

A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject.

Proper citation: ALVIN (RRID:SCR_009527) Copy   

•   Source: SciCrunch Registry