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http://gforge.dcn.ed.ac.uk/gf/project/limo_eeg/

A matlab toolbox (EEGlab compatible) allowing the processing of MEEG data using single trials and hierarchical linear models. Almost all statistical designs can be analyzed with the tool. Across subject analyses are performed using bootstrap offering robust inferences.

Proper citation: LIMO EEG (RRID:SCR_009592) Copy   

•   Source: SciCrunch Registry

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

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

This module reduces Rician noise on nhdr/nrrd DWIs. Filters image in mean squared error sense using Rician noise model. All estimations are performed as sample estimates in a "shaped neighborhood" defined by the weights extracted from structural similarity of voxels following same idea as in Non-Local Means filter.

Proper citation: Joint Anisotropic LMMSE Filter for Stationary Rician noise removal in DWI (RRID:SCR_009502) Copy   

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http://www.cise.ufl.edu/~abarmpou/lab/fanDTasia/

A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

Proper citation: fanDTasia Java Applet: DT-MRI Processing (RRID:SCR_009624) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/~jbm/jip/

Software toolkit for analysis of rodent and non-human primate fMRI data. The toolkit consists of binary executables, highly portable open-source c code, and image resources that enable 1) Automated registration based upon mutual information (affine, non-linear warps), with flexible control and visualization of each step; 2) visualization of 4-dimensional data using either mosaic or tri-planar display of the z/slice dimension, and integration of a general linear model for graphical display of time series analysis; 3) A simple and flexible 1st-order GLM for fMRI time series analysis, a 1st-order GLM analysis for PET data within the SRTM framework, plus a 2nd-order GLM analysis following the Worsley 2002 scheme, and 4) MRI templates to place your rodent and non-human primate data into standardized spaces.

Proper citation: JIP Analysis Toolkit (RRID:SCR_009588) Copy   

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http://www.sph.umich.edu/csg/abecasis/MACH/download/

QTL analysis based on imputed dosages/posterior_probabilities.

Proper citation: MACH (RRID:SCR_009621) Copy   

•   Source: SciCrunch Registry

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

This code registers linearly and non-linearly Diffusion Weighted Magnetic Resonance Images (DW-MRIs) by extending FLIRT (linear registration of 3D scalar volumes) and FNIRT (non-linear registration of 3D scalar volumes) in the FMRIB Software Library (FSL) to work with 4D volumes. The basis for registering DW-MRIs is the concept of Angular Interpolation (Tao, X., Miller, J. V., 2006. A method forregistering diffusion weighted magnetic resonance images. In: MICCAI. Vol. 9. pp. 594?602), which is implemented and extended to non-linear registration, based on the FLIRT and FNIRT models in FSL. See http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2013.00041/abstract. The code does not overwrite FLIRT, FNIRT or any of the FSL C++ code. It is added as FLIRT4D, FNIRT4D and supporting cost functions. The makefiles will however be overwritten to compile the new code, without affecting any version of FSL.

Proper citation: DW-MRI registration in FSL (RRID:SCR_009461) Copy   

•   Source: SciCrunch Registry

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

Tool to assist site staff with curation of data dictionary, data item, and subject item files for preparation to uploading and sharing data with DbGaP resource.

Proper citation: DbGaP Cleaner (RRID:SCR_009462) Copy   

•   Source: SciCrunch Registry

http://www.hammersuite.com/

The tool is a GUI for a complete processing pipeline of brain MR images. It provides functions on skull-stripping, cerebellum removal, tissue segmentation, and HAMMER registration.

Proper citation: HAMMER Suite (RRID:SCR_009583) Copy   

•   Source: SciCrunch Registry

http://econnectome.umn.edu/

An open-source MATLAB software package for imaging brain functional connectivity from electrophysiological signals. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization. Connectivity from EEG/ECoG/MEG can be mapped over sensor and source domains. This package is designed for use by researchers in neuroscience, psychology, cognitive science, clinical neurophysiology, neurology and other disciplines. The graphical interface-based platform requires little programming knowledge or experience with MATLAB. eConnectome is developed by the Biomedical Functional Imaging and Neuroengineering Laboratory at the University of Minnesota, directed by Dr. Bin He. The visualization module is jointly developed with Drs. Fabio Babiloni and Laura Astolfi at the University of Rome La Sapienza.

Proper citation: eConnectome (RRID:SCR_009618) Copy   

•   Source: SciCrunch Registry

http://www.imagilys.com/brainmagix-spm-viewer/

A free, professional viewer for SPM fMRI results. SPM (Statistical Parametric Mapping, UCL, London) is a powerful fMRI analysis software but its visualization capabilities are sometimes a limitation for the researchers. That's why Imagilys has decided to offer the neuroimaging community a free version of its commercial "BrainMagix" neuroimaging software, called "BrainMagix SPM viewer". BrainMagix SPM Viewer's Features - Professional viewer for your SPM-based fMRI activations - JAVA-programmed, cross-platform (Windows, MAC, Linux), without Matlab license, making it possible to share your results with colleagues who do not have SPM installed - Reads SPM.mat files and NIfTI images in an user-friendly way - Overlay the blobs with an atlas or any anatomical image - On the fly adjustment of threshold and cluster size - Localize your activations in an atlas - BOLD signal curves in ROIs (future feature) - Export your results as PNG images

Proper citation: BrainMagix SPM Viewer (RRID:SCR_009537) Copy   

•   Source: SciCrunch Registry

http://en.wikibooks.org/wiki/Pharmacology

Pharmacology is a wikibook covering topics within pharmacology and pharmaceutical sciences.

Proper citation: Pharmacology (RRID:SCR_009017) Copy   

•   Source: SciCrunch Registry

http://web1.sph.emory.edu/bios/CBIS/download_page.php

A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results.

Proper citation: BSMac (RRID:SCR_009531) Copy   

•   Source: SciCrunch Registry

http://www.readout.info

Matlab toolbox that makes it easy to apply decoding analyses to neural data. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and examples are given on how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations.

Proper citation: Neural Decoding Toolbox (RRID:SCR_009012) Copy   

•   Source: SciCrunch Registry

http://pages.stat.wisc.edu/~yandell/qtl/software/qtlbim/

Software library for QTL Bayesian Interval Mapping that provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits. (entry from Genetic Analysis Software)

Proper citation: R/QTLBIM (RRID:SCR_009375) Copy   

•   Source: SciCrunch Registry

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

Program to develop generic standards and tools to facilitate the recording, sharing, and reporting of neuroimaging metadata. It is expected that these efforts will greatly improve upon current practices for archiving and sharing neuroscience data. Neuroscience data, particularly those in neuroinformatics related areas such as neuroimaging and electrophysiology, are associated with a rich set of descriptive information often called metadata. For data archive, storage, sharing and re-use, metadata are of equal importance to primary data, as they define the methods and conditions of data acquisition (such as device characteristics, study/experiment protocol and parameters, behavioral paradigms, and subject/patient information), and statistical procedures. A further challenge for datasharing is the rapidly evolving nature of investigative methods and scientific applications.

Proper citation: INCF Neuroimaging Data Sharing (RRID:SCR_009497) Copy   

•   Source: SciCrunch Registry

http://www.cori.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 5, 2022. Endoscopic Reporting Software, aggregated and individual research data and tailor-made services aimed to advance the overall practice of endoscopy. It was developed to study outcomes of gastrointestinal (GI) endoscopic procedures in real life settings, using data obtained from the CORI Endoscopic Reporting Software or from other endoscopic reporting software. Practice sites include hospitals, ambulatory care centers, private practices, universities, and Veteran''''s hospitals (VA''''s). The CORI v4 Endoscopic Reporting Software is a specialty Electronic Health Record used to document endoscopic procedures and provide reporting services to your practice. Data from participating providers is also sent to a central data repository to become part of the National Endoscopic Database (NED), which now contains data from over 2.7 million GI procedures. The CORI v4 Endoscopic Reporting Software offers significant benefits for participating practices, providers and patients, as well as for everyone who benefits from CORI''''s research efforts. You may actively participate in research with CORI. If you have ideas for research using the NED, their research team can help you evaluate those ideas, collect and analyze the data. In addition, you may choose to participate in one of the prospective research projects conducted by CORI research staff.

Proper citation: Clinical Outcomes Research Initiative (RRID:SCR_009010) Copy   

•   Source: SciCrunch Registry

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

Suite of tools for brain image analysis. Image manipulation, 2D visualization, linear alignment, BBSI, template-based bias correction, skullstrip. GUI Image analysis tools. Now modified to read/write single file nifti (.nii) format. Other packages to be added.

Proper citation: IDeA Lab brain image processing suite (RRID:SCR_009495) Copy   

•   Source: SciCrunch Registry

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

A method for group-wise image registration by pairwisely registering similar images identified using graph theoretic techniques. Particularly, they use sparse coding to estimate image similarity measures among images to be registered, yielding asymmetric, group-wise image similarity measures for each image to others in the group.

Proper citation: Groupwise Image Registration Toolbox (RRID:SCR_009492) Copy   

•   Source: SciCrunch Registry

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

An international effort to establish resources necessary to study the application of neuroimaging measures as (surrogate) biomarkers in Huntington''s Disease (HD). The primary aims are to develop and apply software tools, imaging protocols, quality control procedures, data archiving, data distribution, and participation guidelines that will accelerate existing and prospective imaging studies.

Proper citation: HD Neuro-Informatics (RRID:SCR_009493) Copy   

•   Source: SciCrunch Registry