Tools   Select Another Resource Report Type

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

A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.

Proper citation: freesurfR (RRID:SCR_014110) Copy   

•   Source: SciCrunch Registry

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

A multivariate method for fMRI data analysis based on generalized canonical correlation analysis (gCCA) to maximize SPM reproducibility without adopting any model for the hemodynamic response or other temporal brain responses. For multiple subjects, gCCA explores a broad range of temporal responses in fMRI time-series space while maximizing the mean of correlation coefficients between the pair-wise spatial maps of the subjects.

Proper citation: gCCA (RRID:SCR_014113) Copy   

•   Source: SciCrunch Registry

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

A software application that calculates and runs a GLM on graph theory properties derived from brain networks. The GLM accepts continuous and categorical between-participant predictors and categorical within-participant predictors. Significance is determined via non-parametric permutation tests. Both fully connected and thresholded networks are tested. The toolbox also provides a data processing path for resting state and (block design) task fMRI data. Options for partialing nuisance signals include local and total white matter signal and PCA of white matter/ventricular signal. For task fMRI, connectivity matrices are computed for each condition by dividing up the timeseries. To compensate for HDR-related delay, the timeseries is deconvolved, allowing for division at the actual onset/offset times.

Proper citation: Graph Theory GLM (GTG) MATLAB Toolbox (RRID:SCR_014075) Copy   

•   Source: SciCrunch Registry

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

A user-friendly graphical-user-interface (GUI)-based toolbox (MATLAB) for comprehensive graph-theoretical analyses of brain connectivity, including network construction and characterization, statistical analysis on network topological measures, and interactive exploration of results.

Proper citation: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity (RRID:SCR_014117) Copy   

•   Source: SciCrunch Registry

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

A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.

Proper citation: HAMMER: Deformable Registration (RRID:SCR_014118) Copy   

•   Source: SciCrunch Registry

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

An MRI preprocessing pipeline built with HOF (Heterogeneous Optimization Framework) methodology. MGA prepares neuro-oncology clinical imaging studies for scientific analysis in both longitudinal and cross-sectional studies. It works on DICOM images from a single MRI study and includes perfusion (DSC sequence based) analysis and DTI analysis. MGA spatially co-registers all study images to an atlas template and to a template image within the study.

Proper citation: MGA - Multimodal Glioma Analysis (RRID:SCR_014122) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/bic-mni-models/

Anatomical brain template library which includes models from ICBM 2009 template.Number of unbiased non-linear averages of MNI152 database have been generated that combines attractions of both high-spatial resolution and signal-to-noise while not being subject to vagaries of any single brain. Procedure involved multiple iterations of process where, at each iteration, individual native MRIs were non-linearly fitted to the average template from previous iteration, beginning with MNI152 linear template.

Proper citation: bic-mni-models (RRID:SCR_014087) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/iukf_2013/

A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers.

Proper citation: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 (RRID:SCR_014127) Copy   

•   Source: SciCrunch Registry

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

A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal).

Proper citation: Turbo-BrainVoyager (RRID:SCR_014175) Copy   

•   Source: SciCrunch Registry

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

A tool for visualizing displacement fields estimated in association with image registration. Based on the displacement vector field, a mesh is generated for visualization. The mesh can be color mapped with the jacobian determinant at each point for better localization of regions that undergo compression or expansion. Other key features include: view synchronization, adjustable mesh resolution, and conversion from deformation and HAMMER displacement fields.

Proper citation: Displacement Field Viewer (RRID:SCR_014101) Copy   

•   Source: SciCrunch Registry

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

A GUI-based software for real-time fMRI processing, multivoxel pattern decoding and neurofeedback. The package integrates routines for image preprocessing in real-time, ROI-based feedback and brain decoding-based feedback using the FSL and libSVM libraries. Users can create or employ pre-specified visual stimuli for neurofeedback experiments. FRIEND can be used as Windows standalone software or as a multiplatform toolbox (called FRIEND Engine).

Proper citation: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) (RRID:SCR_014186) Copy   

•   Source: SciCrunch Registry

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

A tool which implements a functional analysis pipeline for the joint analysis of longitudinally measured functional data and clinical data (for example age, gender and disease status). FMPM consists of a functional mixed effects model for characterizing the association of functional response with covariates of interest by incorporating complex spatial–temporal correlation structure, an efficient method for spatially smoothing varying coefficient functions, an estimation method for estimating the spatial– temporal correlation structure, a test procedure with local and global test statistics for testing hypotheses of interest associated with functional response, and a simultaneous confidence band for quantifying the uncertainty in the estimated coefficient functions.

Proper citation: Functional Mixed Processes Models (RRID:SCR_014187) Copy   

•   Source: SciCrunch Registry

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

This resource provides simulated DW-MRI brain images and quantitative tools for evaluating the performance of diffusion analysis methods in terms of fiber orientation estimation and false-positive/-negative fiber rates, which are of fundamental importance to tractography based studies. DW data was generated using a multi-tensor model at SNRs of 9, 18 and 36, for sets of 20, 30, 40, 60, 90 and 120 gradient directions. For each combination of SNR and gradient direction set, 10 realizations of data are provided. All data is simulated with a diffusion-weighting of b=1000, as is common for clinical acquisitions.

Proper citation: Simulated DW-MRI Brain Data Sets for Quantitative Evaluation of Estimated Fiber Orientations (RRID:SCR_014168) Copy   

•   Source: SciCrunch Registry

http://www.theuais.org

A topical portal for the UAIS Lab of Lanzhou University which researches predicting depression and schizophrenia based on demographics and physiological information (EEG, ERPs, Genetics, MRI, fMRI, etc.). It also researches wearable bio-signal sensors and antennas, bio-signal processing, speech analysis, pervasive mental health, psycho-physiological computing, bioinformatics and multimodal data fusion and modeling.

Proper citation: Prediction and Diagnosis for Depression and Schizophrenia (RRID:SCR_014161) Copy   

•   Source: SciCrunch Registry

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

OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

Proper citation: MIView (RRID:SCR_000413) Copy   

•   Source: SciCrunch Registry

https://dipy.org/

Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.

Proper citation: Dipy (RRID:SCR_000029) Copy   

•   Source: SciCrunch Registry

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

Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results.

Proper citation: RapidArt (RRID:SCR_000422) Copy   

•   Source: SciCrunch Registry

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

A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces.

Proper citation: BrainFX (RRID:SCR_000302) Copy   

•   Source: SciCrunch Registry

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

A sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a stable structure of reference can be used without the simple best fit of all surfaces.

Proper citation: CMFreg (RRID:SCR_000171) Copy   

•   Source: SciCrunch Registry

http://nrg.wustl.edu/software/dicom-browser/

A platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. DicomBrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation.

Proper citation: DicomBrowser (RRID:SCR_000864) Copy   

•   Source: SciCrunch Registry