Aims to assists users in spotting and displaying electrodes in patients treated with deep brain stimulation (DBS). Lead-DBS is a program that gathers tools facilitating DBS electrode reconstructions and related processing. This toolkit works by using 3D visualization mode and electrode reconstruction algorithms. It includes the following features: (1) reconstruction of the electrode trajectories; (2) manual correction of the electrode localization; or (3) visualization of a 3D model showing DBS electrodes and their target areas.
Hosts a Simulated Brain Database (SBD) and allows users to run custom MRI simulations with any of several pulse sequences and source digital phantoms, and arbitrary values of the acquisition artifacts. BrainWeb database contains a set of realistic magnetic resonance imaging (MRI) data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known. The SBD contains simulated brain MRI data based on two anatomical models: normal and multiple sclerosis (MS). For both of these, full 3-dimensional data volumes have been simulated using three sequences (T1-, T2-, and proton-density- (PD-) weighted) and a variety of slice thicknesses, noise levels, and levels of intensity non-uniformity. These data are available for viewing in three orthogonal views (transversal, sagittal, and coronal), and for downloading.
Allows users to perform image-based hemodynamics simulation. SimVascular is an open source software which provides a pipeline from model construction to simulation analysis. The software authorizes image processing, segmentation, meshing, as well as an interactive displaying of the results including point cloud visualization and volume rendering. It can be useful for cardiovascular basic science and clinical research and bioengineering education.
A software framework to create 3D finite element models of the left ventricle from cardiac ultrasound or magnetic resonance imaging (MRI) data. The framework is hardware vendor independent and uses speckle tracking (endocardial border detection) on ultrasound imaging data in the form of DICOM. Standard American Heart Association segment-based strain analysis can be performed using a browser-based interface. The speckle tracking, border detection and model fitting methods are implemented in C++ using open-source tools. They are wrapped as web services and orchestrated via a JBOSS-based application server.
Allows to create a high-quality, matched template for a pediatric sample, based on the statistical analysis of a large, healthy pediatric reference population. The Template-O-Matic Toolbox has been updated to run in SPM8. It allows the user to generate customized priors for "classical" unified segmentation (GM, WM, CSF, and T1) as well as for "new segment" (GM, WM, CSF, T1 plus 3 non-brain tissue classes in a single .nii-file). This version also includes an integrated update algorithm that allows easy access to possible updates and fixes.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Permits the incorporation of high-performance soft tissue simulation capabilities into biomedical application. NiftySim is based on the total Lagrangian explicit dynamics (TLEDs) algorithm. It contains (i) membrane and shell formulations compatible with TLED’s explicit time integration; (ii) specialized contact models and; (iii) a general-purpose mesh-based contact model with a collision response formulation. This tool uses GPU technology for biomechanical simulation research in medical image computing, surgical simulation and surgical guidance applications.
Permits modeling of transcranial electrical stimulation (TES). ROAST employs the volumetric segmentation from SPM. It processes individual magnetic resonance imagery (MRI) volumes in a fully automated fashion to generate 3D renderings of the resulting current distributions. This tool divides the full head, arranges virtual electrodes, returns a finite element model (FEM) mesh and solves for voltage and electric field distribution.
Offers researchers a magnetic resonance imaging (MRI) simulation program. SIMRI simulates the physical phenomenon of an MRI acquisition to generate a realistic MRI image. It considers the main static field value and allows realistic simulations of the chemical shift artifact. This software is built on the Bloch equation resolution and integrates an interactive interface for pedagogical purpose based on 1D simulation.
Allows users to modify and fuse heterogeneous breast phantoms to whole-body voxel models. Breast-body-fusion includes three dimensional (3D) resizing, placement with respect to the whole-body voxel model, and voxel extrusion and subtraction to fuse all peripheral breast phantoms with the whole-body voxel model. The software also be used for other regions as well as tumors, patient-specific features or richly-detailed extremity phantoms.
Provides a repository for image-based modeling of blood vessels. vmtk was developed to works easily with images and meshes. It allows users to proceed 3D reconstruction, surface data analysis and mesh generation. The software permits to generate segmentation of vascular segments from medical images. Besides, users can also performs a geometric analysis and surface data processing of 3D models of blood vessels.
Serves for three-dimensional design and modelling. Materialise Mimics is an image processing software that can be used for creating 3D surface models from stacks of 2D image data. It can calculate surface 3D models from stacked image data. This tool is useful to represent the patient’s anatomy in a virtual 3D model and to increase the quality patient care.
Provides a list of tools to aid researchers in reading, interpreting, reporting, and treatment planning. Visible patient includes detection and labeling tools of organ segments. It contains basic imaging tools for: (1) general images; (2) including 2D viewing, (3) volume rendering and 3D volume viewing, (4) orthogonal Multi-Planar Reconstructions (MPR), (5) image fusion, (6) surface rendering, (7) measurements, (8) reporting, (9) storing, (10) general image management; and (11) administration.
Allows users to handle neural networks that uses Theano software. Cortex is a framework that acts as a complement by permitting the training and the evaluation of networks. The application also includes tools for neuroimaging. It was also designed to be very customizable. It can support multiple models such as neuroimaging datasets, feed forward networks or Helmholtz machines as well as variational inference methods.
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