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A practical diffusion MRI simulator for development, testing, and optimisation of novel MR pulse sequences for microstructure imaging. MISST is based on a matrix method approach and simulates the signal for a large variety of pulse sequences and tissue models. It is designed for diffusion MRI researchers who are interested in understanding and developing diffusion pulse sequences for imaging microstructure.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Sample data in MINC format and collection of scripts to verify correct installation of minc-toolkit.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A set of MINC-based image processing tools packaged together. It includes MINC, N3, BICPL, EBKTS, ANIMAL, INSECT, BEaST, Register, Display, and xdisp.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software which provides the automatic solutions for efficent segmentation/labeling anatomcial structures from medical images. It has integrated several multi-atlas based segmentation methods such as majority voting, local weighted voting, and non-local patch based segmentation methods.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

The Longitudinal MS Lesion Imaging Archive provides Training data consisting of longitudinal images from five patients and Testing data consisting of 15 patients. Each longitudinal dataset includes T1-weighted, T2-weighted, PD-weighted, and T2-weighted FLAIR MRI with 3-5 time points acquired on a 3T MR scanner. T1-weighted images have approximately a 1mm cubic voxel resolution, while the other scans are 1mm in plane with 3mm sections. Accounting for the multiple time points, this constitutes approximately 80 individual data sets. The Training data contains manual segmentations of the MS lesions from two different raters for each of the time points provided.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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

Journals addressing functional and structural neuroimaging topics.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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

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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

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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.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen