Curator Dashboard

A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A programming library to help users read, write, manipulate, translate, and validate SBML files and data streams. Specifically, it is a library that users may embed into their own applications.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A filter which allows the Laplace-Beltrami operator to determine surface harmonics in terms of PointData at each vertex. It determines the requested N most significant harmonics of a surface.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A program which creates anatomically realistic virtual neurons using the formalism of the Lyndenmayer systems to implement sets of neuroanatomical rules discovered by several research groups. The program algorithms read in experimental data - in the form of statistical distributions - to generate virtual structures. L-Neuron samples the values of the parameters within these statistical distributions in a stochastic (random) fashion during dendritic growth.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software which aims to better estimate the neuronal activation of an individual using the results of an independent component analysis (ICA) method applied to a temporally concatenated group of functional magnetic resonance imaging (fMRI) data (i.e., Tc-GICA method). This approach employs iterative LS solutions to refine both the individual SPs and TCs with an additional a priori assumption of sparseness in the SPs (i.e., minimally overlapping SPs) based on L(1)-norm minimization.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A diffusion MRI service that handles the processing of diffusion data from raw data to structural connectivity. They provide high angular resolution (HARDI) reconstruction from DTI data with at least 20 gradient directions acquisitions.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A collection of software tools developed for medical image synthesis of typically magnetic resonance (MR) brain images. The approaches have been used to create computed tomography (CT) images from MR input. The goal of image synthesis is to recover MR images with a desired optimal contrast for further processing by either registration or segmentation.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A project which contains data and analysis pipelines for a set of 53 subjects in a cross-sectional Parkinsons disease (PD) study. The dataset contains diffusion-weighted images (DWI) of 27 PD patients and 26 age, sex, and education-matched control subjects. The DWIs were acquired with 120 unique gradient directions, b=1000 and b=2500 s/mm2, and isotropic 2.4 mm3 voxels. The acquisition used a twice-refocused spin echo sequence in order to avoid distortions induced by eddy currents.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A collection of software tools for high dimensional brain imaging genomics. These tools are designed to perform comprehensive joint analysis of heterogeneous imaging genomics data. HDBIG-SR is an HDBIG toolkit for sparse regression while HDBIG-SCCA is an HDBIG toolkit for sparse association.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A MATLAB toolbox for denoising task-based fMRI data. It derives noise regressors from voxels unrelated to the experimental paradigm and uses these regressors in a general linear model (GLM) analysis of the data. The technique only requires a design matrix indicating the experimental design and an fMRI dataset.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen