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BET / Brain Extraction Tool
Deletes non-brain tissue from an image of the whole head. BET can also estimate the inner and outer skull surfaces, and outer scalp surface, if T1 and T2 input images are of good quality. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of magnetic resonance sequences. BET uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre-processing before being applied. BET takes about 5-20 sec to run on a modern desktop computer and is freely available, as a standalone program that can be run from the command line or from a simple GUI, as part of FSL (FMRIB Software Library).
Recovers accurate quantitative radioactivity concentration in Positron Emission Tomography (PET) images. SFSRR combines functional and structural information from a number of sources such as computerized tomography (CT), Magnetic Resonance Imaging (MRI) and anatomical probabilistic atlases. It is based on the multiresolution property of the wavelet transform. It is able to incorporate standardized anatomical information. The tool was validated on a digital Zubal phantom and clinical data to evaluate its quantitative potential.
N3 / Non-parametric Non-uniform intensity Normalization
Adjusts intensity non-uniformity in 3D magnetic resonance (MR) images. N3 models non-uniformity as a smooth multiplicative field to obtain an approximation of the tissue dependent character of excitation field non-uniformity. It allows violations of the stationarity assumption and considers that the image intensities are independent identically distributed random variables. It uses also and iterative method to assess the distribution of the true tissue intensities and the multiplicative bias field.
AMIDE / Amide's a Medical Imaging Data Examiner
Displays and analyzes multimodality volumetric medical images. AMIDE provides the research community with a relatively full-featured, freely available, and open source solution for single and multimodality volumetric medical image analysis. It provides a variety of additional features useful to the molecular imaging researcher, including fully three dimensional ROI drawing and analysis for static and dynamic images, two and three way linked viewing (dual cursor mode), rigid body registration using fiducial markers, filtering and cropping of data sets, movie generation, series viewing, and volume rendering.
Amira 3D Software for Life Sciences
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
TORTOISE / Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble
Processes the diffusion of magnetic resonance imaging (MRI) data. TORTOISE contains three main modules: DIFF_PREP-software for image resampling, motion, eddy current distortion, and EPI distortion correction using a structural image as target, and for re-orientation of data to a common space; DIFF_CALC-software for tensor fitting, error analysis, directionally encoded color map visualization and ROI analysis; DR-BUDDI-software for EPI distortion correction using pairs of diffusion data sets acquired with opposite phase encoding (blip-up blip-down acquisitions).
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