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http://www.temporal-lobe.com/

Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection.

Proper citation: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat (RRID:SCR_002816) Copy   

•   Source: SciCrunch Registry

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

VUIIS (Vanderbilt University Institute of Imaging Science) Image and Data Analysis Core's data processing tools written for MATLAB and, unless stated otherwise, capable of processing 2D/3D images (matrices). These tools are written for ease of use from within MATLAB.

Proper citation: vuTools (RRID:SCR_001704) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/DOT/resources/tmcimg/

Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.

Proper citation: Monte Carlo Simulation Software: tMCimg (RRID:SCR_002588) Copy   

•   Source: SciCrunch Registry

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

Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.

Proper citation: TumorSim (RRID:SCR_002604) Copy   

•   Source: SciCrunch Registry

http://www.pstnet.com/software.cfm?ID=96

Designed for use in an MRI simulator, MoTrak software uses Ascension Technology?s Flock of Birds. The sensor attaches to the subject?s head and determines the position of the head in space relative to the transmitter. The sensor records angular rotations as well as positional displacements from an initially calibrated position. This information is displayed and logged by the program in real-time, allowing observation of head motion in an MRI simulator. In the simulator, the participant can simultaneously be habituated to the MRI environment, while being trained to remain still via feedback from the MoTrak system.

Proper citation: MoTrak Head Motion Tracking System (RRID:SCR_009607) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/hfh_t1_hp_seg1/

Shared dataset which consists of skull-stripped T1 MRI images and segmented hippocampi of 163 Temporal Lobe Epilepsy (TLE) patients. The T1 and hippocampal segmentation data of TLE patients are uploaded in three separate datasets which can be accessed from the main site.

Proper citation: Epilepsy T1 and Hippocampal Segmentation Datasets (RRID:SCR_014926) Copy   

•   Source: SciCrunch Registry

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

Behavioral and imaging data from about 120 participants aged 18-89. Data were collected as part of a grant to use high-resolution imaging and advanced behavioral tasks to understand how aging affects the hippocampus and how this is related to age-related cognitive decline. The full dataset includes traditional neuropsycholgical measures, hippocampal-specific behavioral measures, whole-brain DTI, high-resolution DTI of the medial temporal lobes, and structural MRI including segmentation of grey/white/CSF, of cortical regions and of hippocampal subfields.

Proper citation: Stark Cross-Sectional Aging (RRID:SCR_014171) Copy   

•   Source: SciCrunch Registry

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

A dataset which contains diffusion tensor images of 93 healthy, young male subjects.

Proper citation: YMDTI: Diffusion Tensor Images of Healthy Young Males (RRID:SCR_014183) Copy   

•   Source: SciCrunch Registry

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

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

Proper citation: Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) Copy   

•   Source: SciCrunch Registry

http://micro-manager.org

Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

Proper citation: uManager (RRID:SCR_000415) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/meshmetric3d/

Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.

Proper citation: 3DMeshMetric (RRID:SCR_000043) Copy   

•   Source: SciCrunch Registry

http://www.talairach.org/

Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

Proper citation: Talairach Daemon (RRID:SCR_000448) Copy   

•   Source: SciCrunch Registry

http://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry

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

Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach and education The ATP is not a clinical organ procurement agency, but rather they facilitate the wishes of donors and families to donate their tissue to autism research. Through the ATP's established international infrastructure, they work with any accredited tissue bank, organ procurement agency, or medical examiner that receives a family's request to donate their loved one's tissue to the program. Once contacted, the ATP will insure that the family's request to donate their loved one's tissue is faithfully met, covering all costs to the family and partnering agency as well as ensuring the tissues' proper and rapid transport to the ATP's repository at the Harvard Brain Tissue Resource Center (HBTRC) in Boston, Massachusetts.

Proper citation: Autism Tissue Program (RRID:SCR_000651) Copy   

•   Source: SciCrunch Registry

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

Construct and analyse brain network is a brain network visualization tool, which can help researchers to visualize construct and analyse resting state functional brain networks from different levels in a quick, easy and flexible way. Entrance parameter of construct and analyse brain network is export parameters of dparsf software.It would be greatly appreciated if you have any suggestions about the package or manual.

Proper citation: BrainNetworkConstructionAnalysisPlatform (RRID:SCR_000854) Copy   

•   Source: SciCrunch Registry

http://fcp-indi.github.io

A configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion?without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.

Proper citation: C-PAC (RRID:SCR_000862) Copy   

•   Source: SciCrunch Registry

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

An I/O library for Matlab/Octave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression. More information and code examples at: http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

Proper citation: cbiNifti: Matlab/Octave Nifti library (RRID:SCR_000860) Copy   

•   Source: SciCrunch Registry

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

Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know!

Proper citation: Philips Users Community (RRID:SCR_001438) Copy   

•   Source: SciCrunch Registry

http://incf.org/programs/atlasing/projects/waxholm-space

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.

Proper citation: Waxholm Space (RRID:SCR_001592) Copy   

•   Source: SciCrunch Registry

http://neuro.imm.dtu.dk/wiki/Main_Page

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format.

Proper citation: Brede Wiki (RRID:SCR_001411) Copy   

•   Source: SciCrunch Registry