Morphology measurement software tools | Magnetic resonance imaging analysis

Allows users to work about magnetic resonance imaging (MRI) brain imaging data. FSL can realize functional magnetic resonance imaging (FMRI) analysis (brain extraction, smoothing, statistics, registration). This tool can analyze a wide range of MR modalities (task FMRI, resting FMRI, ASL, diffusion, structure), and can be easily scripted and run over computing clusters.

Allows construction of a similarity measure between brain scans. BrainPrint facilitates the statistical analysis by computing distances between shape descriptors without the need for establishing direct correspondences. It focuses entirely on the geometric properties of the brain and consequently it is a characterization that is robust to intensity variations between scans. This tool is especially beneficial when working with large datasets.

A fully automated feature-matching approach to assign anatomical labels to cortical structures and activity in human brain magnetic resonance images (MRI) data. Mindboggle employs each atlas in a database independently to label the cortical voxels of a subject brain image and for each voxel chooses the majority label assigned by the different atlases. Ultimately, Mindboggle software can provide confidence measures for labels based on probabilistic assignment of labels and could be applied to large databases of brain images.

Enables largely automated processing of magnetic resonance images (MRI) of the human brain. BrainSuite provides a sequence of low-level operations that can produce accurate brain segmentations in clinical time. It produces classified brain volumes that can be useful for quantitative studies of different regions of the brain. The tool consists of several modules that performs skull and scalp removal, nonuniformity correction, tissue classification, and object topology correction.

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).

Derives root structural architecture (RSA) parameters for 3D magnetic resonance imaging (MRI) images of soil grown plant roots. NMRooting can achieve automated analysis of MRI datasets. This software measures root traits from the collected images including root mass, lengths, diameters, angles, and number of root tips. It can be useful for the investigation on dynamic effects of stress or changing environmental conditions on live root systems.

Allows users to study and visualize clinical/anatomical correlations and brain deficits in Human Immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS). JRD-fluid is an analysis method using fluid image warping. It consists of information-theoretic measure of image correspondence. It assists users to work about AIDS neuropathology. This algorithm is also useful for studies that concern neuroscientific topic.

Allows ultra-high-resolution brain segmentation at 7 Tesla (T). CBS Tools is an automated computational framework for brain segmentation and cortical reconstruction at the ultra-high resolution of 0.4 mm, based on quantitative T1 images acquired at 7 T with the MP2RAGE sequence. The software is implemented as a plug-in for the MIPAV and JIST medical image processing platforms. It supports many image formats, and includes a user-friendly interface for image visualization and editing as well as a graphical pipeline engine for large-scale processing.

Calculates the fractal dimensionality of a 3D structure. calcFD is designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes. The toolbox includes options to use different masking files and is implemented to use either the box-counting or dilation algorithms and to use either the filled volume or just the surface of the structure. The toolbox can easily be run on all of the participants in a FreeSurfer subject folder, or just on specified subject folders. The Matlab toolbox also includes several functions designed to improve functionality, such as the automatic ‘cropping’ of the volume space to the smallest bounding box necessary to contain the volume, improving computation time drastically. Example files are also provided to aid in using the toolbox for the user‘s needs.

Enables rapid identification of phenotypically abnormal structures. Data are easily loaded by drag and drop, with support for most commonly used file formats. On loading the registration results, embryos may be overlaid with the t-statistic heatmaps to reveal regions of dysmorphology. We have adopted a hot red/blue colour scheme to be consistent with previously reported results. The heatmap data can be filtered by t statistic value to emphasize regions of different statistical significances. Vector field data can also be loaded into VPV and filtered by magnitude to identify where the most significant deformations have taken place during registration.

A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and particulate parameters in a convenient format. Java technology allows BoneJ to run on commodity computers, independent of scanner devices, fully utilising hardware resources. ImageJ’s plugin infrastructure provides a flexible working environment that can be tailored to diverse experimental setups. BoneJ is a working program and a starting point for further development, which will be directed by users’ requests and the emergence of new techniques.

Allows users to quantify morphometric and intensity features of intracranial arteries on MR angiography (MRA) images. iCafe provides a graphic interface for measuring information on large or/and small arteries to possibly correlate perfusion imaging. The software performs multiple features such as image preprocessing, vessel tracing, or artery labeling. It aims to help in investigating quantitative intracranial vascular research.

Automates regional behavioral analysis of human brain images. Mango provides analysis tools and a user interface to navigate image volumes. The tool is ease to use, multi-platform Java application and extensive region of interest tools. It has the ability to add and update software as a plugin module and offers full access to a suite of image viewing and processing features. The software is able to rapidly determine regionally specific behaviors for researchers’ brain studies.

Enables easy pattern classification of neuroimaging data and offering a broad assortment of machine learning algorithms and feature selection methods. MANIA provides interfaces to common third party software libraries, especially Matlab pattern classification tools. It is easy to use for non-experts, users are encouraged to study the basics of the different methods especially when using advanced and complex algorithms.

Accesses age prediction models created by using machine learning based analysis of neuroimaging data. NAPR system allows external users to predict the age of individual subjects using their own MRI data. The approach will allow for rigorous evaluation and comparison of age prediction methods and ultimately lead to age prediction models that are accurate enough to be utilized for clinical applications. It provides a system for out-of-sample model testing, which is the most rigorous model evaluation technique available.

Allows detailed investigation and evaluation of multidimensional biomedical images. AnalyzePro can serve for magnetic resonance imaging, radionuclide emission tomography, ultrasound tomography, and 3-D imaging modalities based on x-ray computed tomography. It contains features for interactive display, manipulation and measurement of multidimensional image data.

Derives extensive panels of quantitative imaging phenomics (QIP) features and integrates them into non-invasive diagnostic and predictive models. CaPTk simplifies the clinical translation of complex algorithms. It extracts spatial patterns of cancer distribution, obtained via deformable registration methods. This tool operates quantitative analyses in a straightforward manner without requiring a substantial computational background.

Processes fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data (MRI). CIVET performs transformation into stereotaxic space, gray and white matter tissue classification, reconstruction of left and right hemisphere cortical surfaces, surface registration in order to perform group comparisons and cortical thickness analysis. Regional maps are produced based on the lobar parcellation of surfaces. A number of other measurements are also performed, such as mean curvature, gyrification index and total cortical area. CIVET is available via the CBRAIN interface which allows users to configure and run CIVET on large datasets.

Processes multiple different analysis on magnetic resonance imaging (MRI) data such as functional MRI and diffusion MRI. VISTASOFT contains several modules that allows users to: align functional and anatomical data, display MR data on rendered 3D surface representations of the brain, handle anatomical MRI data, analyze functional MRI data or provide a list of scripts.

Hosts heterogeneous tools dedicated to neuroimaging research. BrainVISA aims to help researchers in developing new neuroimaging tools, sharing data and distributing software. It offers a way to define viewers which may use any visualization software. Thanks to its data management functions, the tool can define the data types handled by the software, associate key attributes for indexation, and filename patterns to make the link between the filesystem and the database schema.

Allows users to display multiplanar, orthogonal views, volume and surface renderings with thresholding-based tissue segmentation. 3DimViewer is a lightweight 3D viewer of medical digital imaging and communications in medicine (DICOM) datasets. It contains several features such as: distance and density measuring, high quality volume rendering for direct 3D visualization, surface reconstruction of any segmented tissue, or 3D surface rendering.

Permits three-dimensional (3D) measurement and volume visualization. VoxBlast consists of a general-purpose rendering application for research. It furnishes functions for pseudo- coloring, transparency, lighting, 2D and 3D measurements, 2D slice viewing, cropping, seed fill, movie loop generation, filters, palette editing, surface extraction and polygon rendering. This tool is designed for computed tomography (CT) scans, magnetic resonance (MR) scans, or microscope data.

Consists of a library designed for volume rendering. VolPack supports user-specified transfer functions for both opacity and color. It furnishes a shading model with directional light sources, multiple material types with several reflective properties, depth cueing, and shadows. This tool can be employed to arbitrary affine view transformations. It constructs color or grayscale renderings.

Offers a platform for fractal analysis and morphology functions. FracLac is a module that can be used as an ImageJ or FIJI plugin. The application includes features such as: (i) analyzing complexity and heterogeneity, (ii) measuring difficult to describe geometrical forms; (iii) extracting of pattern from several types of images for analysis. The software is suitable for images of biological cells as well as for other structures such as branching structures or known fractals.

Offers a set of methods for computational anatomy. CAT extends segmentation methods supplied by the SPM software by furnishing two approaches to reduce noise, an internal interpolation as well as multiple techniques encompassing local adaptive segmentation (LAS). The application enables application in: (i) voxel-based morphometry (VBM); (ii) deformation-based morphometry (DBM); (iii) region- or label-based morphometry (RBM) as well as (iv) surface-based morphometry (SBM).

Provides a common visualization and storage platform, which can be used for visualization of data from any source, provided that an import filter exists for this format. This platform can be extended by various software packages, individually designed for analysis of specific data sets. Visualization is based on multi-planar reconstruction allowing extraction of arbitrary slices from a 3D-volume.

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.