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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.nitrc.org/projects/vmagnotta/

A Diffusion Tensor fiber tracking software suite that includes streamline tracking tools. The fiber tracking includes a guided tracking tool that integrates apriori information into a streamlines algorithm. This suite of programs is built using the NA-MIC toolkit and uses the Slicer3 execution model framework to define the command line arguments. These tools can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3. NOTE: All new development is being managed in a github repository. Please visit, https://github.com/BRAINSia/BRAINSTools

Proper citation: GTRACT (RRID:SCR_009651) Copy   

•   Source: SciCrunch Registry

http://www.restfmri.net

A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files.

Proper citation: REST: a toolkit for resting-state fMRI (RRID:SCR_009641) Copy   

•   Source: SciCrunch Registry

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

Quadratically constrained quadratic programing (QCQP) technique in medical image analysis. QCQP based tools are provided for classification, segmentation, and bias field correction.

Proper citation: QCQP (RRID:SCR_009640) Copy   

•   Source: SciCrunch Registry

http://beast.bio.ed.ac.uk/

A cross-platform software program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Proper citation: BEAST (RRID:SCR_010228) Copy   

•   Source: SciCrunch Registry

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

Pipeline developed for delineating the association between multiple diffusion properties along major white matter fiber bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these white matter tract properties in various diffusion tensor imaging studies. FADTTS can be used to facilitate understanding of normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. The advantages of FADTTS compared with the other existing approaches are that they are capable of modelling the structured inter-subject variability, testing the joint effects, and constructing their simultaneous confidence bands.

Proper citation: Functional Analysis of Diffusion Tensor (RRID:SCR_008888) Copy   

•   Source: SciCrunch Registry

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

Project hosting binary packaged distributions, scripts, example datasets, and corresponding results of analysis using their UNC/Utah NAMIC DTI Fiber Analysis Framework. This project can be seens as a master project encompassing several current NITRC projects into a coherent set. Their workflow utilizes tools already available on NITRC including: * DTIPrep * DTIAtlasBuilder * FiberViewerLight * DTIAtlasFiberAnalyzer * FADTTS

Proper citation: UNC/Utah NAMIC DTI Fiber Analysis Framework (RRID:SCR_009615) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/fiber-sig/

Used to analyze the fibers produced by ukf tractography

Proper citation: Fiber Tracking Tool (RRID:SCR_009474) Copy   

•   Source: SciCrunch Registry

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

These are the scripts used for the analyses reported in: Craddock RC, Holtzheimer PE, 3rd, Hu XP, Mayberg HS. (2009): Disease state prediction from resting state functional connectivity. Magn Reson Med 62(6):1619-28. Specifically included are scripts for performing t-test filter, reliability filter, recursive feature elimination, and reliability recursive feature elimination feature selection methods. These make use of wrappers that perform .632 bootstrap and k-fold cross validation strategies. The scripts are written in matlab and require the Bioinformatics toolbox. If you do not have the bioinformatics toolbox, the scripts can be easily modified to run with other matlab SVM toolboxes (i.e., libsvm, svmlight, shogun, etc.).

Proper citation: Disease State Prediction (RRID:SCR_009467) Copy   

•   Source: SciCrunch Registry

http://www.nmr.mgh.harvard.edu/DOT/resources/homer2/home.htm

Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data.

Proper citation: Homer2 (RRID:SCR_009586) Copy   

•   Source: SciCrunch Registry

http://www.iit.edu/~mri/

Atlas that contains new anatomical, DTI, HARDI templates and probabilistic gray matter labels of the adult human brain in ICBM-152 space. Artifact-free MRI data from 72 human subjects was used in the development of the atlas. All diffusion MRI data collection was conducted using Turboprop, and spatial normalization was accomplished in a population-based fashion. A description of the contents of the atlas can be found in the Downloads link. NOTE: The files of the older IIT2 DTI Brain Template are still available. However, the new DTI template of the IIT Human Brain Atlas (v.3) is of superior quality and allows more accurate registration across subjects.

Proper citation: IIT Human Brain Atlas (RRID:SCR_009587) Copy   

•   Source: SciCrunch Registry

http://hermes.ctb.upm.es/

A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

Proper citation: HERMES (RRID:SCR_009584) Copy   

•   Source: SciCrunch Registry

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

This is a command line tool which allows the user to study the behavior of water diffusion (using DTI data) along the length of the white matter fiber-tracts. Various tract-oriented scalar diffusion measures obtained from DTI brain images, are treated as a continuous function of white matter fibers'' arc-length. To analyze the trend along a given fiber tract, a command line tool performs kernel regression on this data. The idea is to try out different noise models and maximum likelihood estimates within kernel windows (along the tract), such that they best represent the data and are robust to noise and Partial Volume effect. The package contains several command line based modules and an GUI based tool called DTIAtlasFiberAnalyzer to access most functions. The features available in the tool currently, its use and input / output formats and other relevant details are provided in the first draft of the documentation. (http://www.na-mic.org/Wiki/index.php/Projects:dtistatisticsfibers).

Proper citation: DTI Fiber Tract Statistics (RRID:SCR_009460) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/inia19/

Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas.

Proper citation: INIA19 Primate Brain Atlas (RRID:SCR_009498) Copy   

•   Source: SciCrunch Registry

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

A set of MATLAB scripts for analysis of networks derived from neuroimaging data. Some of these scripts are entirely original, while some are adapted (or just copied) from the Brain Connectivity Toolbox (https://sites.google.com/a/brain-connectivity-toolbox.net/bct) The source code is available via git: git clone ssh://user

Proper citation: Graphtools (RRID:SCR_009490) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/r-spit/

Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

Proper citation: resting-state pediatric imaging template (RRID:SCR_009647) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/factory4t1ndti/

Tools to make easier on using spm, pipedream, dti-tk, and other softwares to analyze t1 or dti images.

Proper citation: factory t1 dti (RRID:SCR_009523) Copy   

•   Source: SciCrunch Registry

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

A graph theoretical network analysis toolbox which allows researchers to perform comprehensive analysis on the topology of brain connectome by integrating the most of network measures studied in current neuroscience field.

Proper citation: GRETNA (RRID:SCR_009487) Copy   

•   Source: SciCrunch Registry

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

A platform for any Principal Component Analysis (PCA)-based analysis on functional neuroimaging data (PET and fMRI). Includes: * Ordinal Trend Canonical Variance Analysis for parametric designs (C. Habeck et al. A New Approach to Spatial Covariance Modeling of Functional Brain Imaging Data: Ordinal Trend Analysis. Neural Computation 2005; 17: 1602-1645) * Partial Least Squares for any design matrix * Subprofile Scaling Model for cross-sectional designs (JR. Moeller, Strother SC. A regional covariance approach to the analysis of functional patterns in positron emission tomographic data.J Cereb Blood Flow Metab. 1991 Mar;11(2):A121-35.)

Proper citation: Generalized Covariance Analysis (RRID:SCR_009488) Copy   

•   Source: SciCrunch Registry