Allows users to estimate the forward and reverse transformation between two images. SICLE is an image registration algorithm that determines the forward and reverse transformation between them while minimizing the inverse consistency error. It acts like that to cut the correspondence between these transformations associated with large inverse consistency errors. The estimated transformations are regularized thanks to a thin-plate spline (TPS) model.
Offers a reference frame for activation labeling. AAL is based on an anatomical parcellation of the Montreal Neurological Institute (MNI) single-subject brain. It makes the correspondence between the coordinates obtained from images normalized with the MNI average template as the target and the Talairach atlas brain. The tool uses the terminology for sulci to parcellate the inferior surface of the frontal lobe corresponding to the orbitofrontal cortex areas. The method aims to suppress the confusion existing in the literature regarding the relationship between a set of coordinates and its anatomical label.
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.
Serves for the automated registration of 3D and 2D images within and across subjects and imaging modalities. AIR offers automated routines for reslicing and aligning tomographic image data. This software includes homologous 2D deformation models and is designed for intersubject registration of 3D human brain data. It offers also nonlinear registration tools for intrasubject registration of developmental data and nonlinear image distortions data.
Provides method to evaluate design choices and to choose parameter values. ANIMAL method assists users to realize comparison between competing spatial normalization algorithms. This method is based on multi-scale, three-dimensional (3D) cross-correlation to record a given volumetric data set to an average Magnetic Resonance Imaging (MRI) brain. Direct comparison of two or more data sets brought into stereotaxic space is allowed by this tool.
Allows the user to quickly configure, test, and compare different registration methods for a specific application. elastix is a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. It has a command-line interface, which simplifies batch-processing of large numbers of data sets. Registration of large 3-D images can be done efficiently, thanks to the use of stochastic subsampling techniques.
Registers nonrigid 3-D breast magnetic resonance imaging (MRI). IRTK is based on normalized mutual information and utilizes a nonrigid transformation model to describe the motion of the breast in dynamic MR images. This tool can be useful for the schematization of the motion of the breast. It permits researchers to minimizes motion artifacts between images significantly.
Allows to study diffusion Magnetic Resonance Imaging (MRI) data. Dipy is a program allowing users to share their code and experiments. One of its objectives is to provide transparent implementations for all the different steps of the dMRI analysis with a uniform programming interface. It implements two interfaces for probabilistic Markov fiber tracking: (1) it allows the user to provide the distribution evaluated on a discrete set of possible tracking directions, and (2) it accommodates tracking methods where the fiber orientation distribution function (fODF) cannot be easily computed.
Allows the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. FreeSurfer proposes a suite of tools that provide extensive and automated analysis of key features in the human brain. This includes skull stripping, image registration, subcortical segmentation, cortical surface reconstruction, cortical segmentation, cortical thickness estimation, longitudinal processing, fMRI analysis, tractography, FreeView Visualization GUI, etc... FreeSurfer is freely available, runs on a wide variety of hardware and software platforms, and is open source.
An alignment procedure by maximizing image contrast across tissue boundaries rather than matching intensities between two images or by matching surface shapes. . BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial brain images to whole brain images, a domain in which existing registration algorithms frequently fail. BBR is part of the FreeSurfer software package.
Computes high-dimensional mappings to capture the statistics of brain structure and function. ANTs allows users to organize, visualize and statistically explore large biomedical image sets. It integrates imaging modalities and related information in space and time, and works across species or organ systems with minimal customization. ANTs depends on the Insight ToolKit (ITK), a widely used medical image processing library to which ANTs developers contribute. ANTs can be used paired with ANTsR, an emerging tool supporting standardized multimodality image analysis. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.
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.
Conducts surface registration from multiple sources of information. MSM represents displacement of each surface vertex in form of a discrete set of possible rotations. It offers a regularization term method specially created for the spherical surface. This tool is based on penalising the geodesic distance between rotation matrices. It has a reduced sensitivity to local minima and includes a multivariate mutual-information measure.
Provides a protocol that enables a thorough, optimization-independent, and systematic statistical evaluation of important similarity measure properties. Evaluation of similarity measures includes Accuracy (ACC), Distinctiveness of the Optimum (DO), Capture Range (CR), Number of Local Minima (NOM), Risk of Non-convergence (RON). The evaluation consists of three steps: (i) sampling of the parametrical space, (ii) computation of similarity measure values and (iii) computation of similarity measure properties.
Constructs deformable brain images. HAMMER can reveal geometric characteristics of the underlying anatomical structures. It employs a hierarchical deformation mechanism and an attribute vector to work. This tool can reflect the geometric properties of the underlying structure from a local scale, to a global scale that reflected spatial relationships with more distant surface points.
Allows estimation of a regularized deformation field between two volumes. ROMEO consists in an algorithm based on optical-flow and implements multiresolution and multigrid minimization scheme to calculate large deformations. The software is based on a dense robust 3-D estimation of the optical flow with a piecewise parametric description of the deformation field.
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.
Permits to visualize electrodes implantation on image data and prepares database for group studies. IntrAnat Electrodes allows users to search across patients according to a variety of anatomical and functional criteria. It uses established research neuroimaging toolboxes such as BrainVisa, Freesurfer, SPM and ANTs to recycle optimal and validated image analysis processes.
Provides a collection of analysis tools for magnetic resonance brain imaging data. MRTool enables spatial registration via a statistical parametric mapping (SPM12) approach. This software is appropriate for the processing of structural magnetic resonance images of brains with cortical atrophy and ventricular enlargement via the use of a nonlinear registration step.
Allows users an estimation of displacement fields for inter-subject registration of high-resolution volumetric magnetic resonance imaging (MRI) images. ART contains an inter-subject registration algorithm that is a non-parametric method. This tool can reduce anatomical variability between subjects. This tool permits the addition of a large number of degrees of freedom, and users can utilize several numbers of basic functions.
A three-dimensional (3D) reconstruction and modeling software. Free-D allows to generate, process and analyze 3D point and surface models from stacks of 2D images. It is an integrated software tool, offering in a single graphical user interface all the functionalities required for 3D modeling.
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.
Offers a workflow dedicated to the management of deep brain stimulation (DBS) surgery. PyDBS allows users to handle patient data from a single database towards three automatic pipelines coupled to their corresponding visualization modules. It provides inclusion preoperative and postoperative pipelines that produces images, masks, meshes, and geometrical transformations. The program does not require patient-specific parameter settings.
Allows the generation of tissue class priors from infancy to old age. CerebroMatic is a toolbox that uses a more flexible statistical approach, namely multivariate adaptive regression splines. It was developed for use within the spm software environment. This method allows user to generate matched tissue probability maps for tissue segmentation and spatial normalization. It is based on statistically-generated regression parameters from a large sample of healthy infants, children, and adults.
Allows to perform registration and segmentation for image analysis. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. ITK uses a model of software development known as Extreme Programming. The sampled representation is an image acquired from such medical instrumentation as Computed Tomography (CT), Magnetic Resonance Imaging (MRI) or ultrasound scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with a MRI scan in order to combine the information contained in both.
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.
Consists of a non-parametric diffeomorphic registration algorithm. Diffeomorphic Demons is an optimization procedure on the entire space of displacement fields. This method can provide non-parametric free-form diffeomorphic transformations.
Provides a high-resolution in vivo magnetic resonance imaging template of the average macaque brain generated from 31 subjects, as well as a neuroimaging tool for improved data analysis and visualization. From the NMT volume, maps of tissue segmentation and cortical thickness were generated. Surface reconstructions and transformations to previously published digital brain atlases are also provided. An analysis pipeline using the NMT automates and standardizes the time-consuming processes of brain extraction, tissue segmentation, and morphometric feature estimation for anatomical scans of individual subjects. The NMT and associated tools thus provide a common platform for precise single-subject data analysis and for characterizations of neuroimaging results across subjects and studies.
Furnishes a deep learning solution for magnetic resonance imaging (MRI) registration quality control (QC). Deep QC can be used for automatic testing of the robustness of image registration methods. It enables users to rerun the registration methods with different settings and parameters to ensure a high acceptance rate for their cohort of interest. However, it can be incorporated into the process of the registration to enforce the method to repeat registration with different parameter settings until an accepted registration is obtained.
Records symmetrically a set of magnetic resonance imaging (MRI) scans of human brain from a single individual over time. ATRA is an algorithm which focuses on providing an automatic registration of serial 3D T1-weighted structural volumes. The method can be applied on different scans derived from a unique scanning session or from scans captured over an extended period of time.
Modulates brain magnetic resonance imaging (MRI) contrasts. MRI2MRI is a solution based on a deep learning algorithm able to capture complex nonlinear and spatially-varying dependencies among MRI contrasts. The application can handle single or multiple images and support the integration of images with different contrasts. It can be employed to analyze multi-modal MRI data.
Performs 2D image registration based on elastic deformations represented by B-splines. bUnwarpJ is an ImageJ plugin that works on registration of two images, A and B: Image A is elastically deformed to look as similar as possible to image B, and, at the same time, the "inverse" transformation (from B to A) is also calculated. As a result, two images are given: the deformed versions of A and B images.
Segments structural magnetic resonance imaging (MRI) data. IBASPM aims to complement the SPM software by providing an atlas registration approach. It offers a set of features dedicated to: (i) spatial normalization; (ii) segments gray/white matter and cerebral spinal fluid tissues; (iii) labellisation; (iv) generate atlases, statistical probability anatomy maps (SPAMs) and MaxProb atlases; (v) compute statistics and individual brain volumes and (vi) visualize results. This program is compatible with SPM2 et SPM5.
Allows to realize analysis and visualisation of 3D biological image data, and more particularly traced neurons. NAT accepts 3D images in NRRD and 'Amira' AmiraMesh formats. The data can be manipulated and visualized in 3D. The manipulation includes applying calculated registrations, e.g. using the 'CMTK' registration suite. This tool permits morphological comparison between neurons including clustering and searching.
Allows users to research and visualize medical images. medInria is a platform for the diffusion of research software in medical imaging created by Inria teams. This platform offers several types of functions such as: (1) management of the database and file importation; (2) 2D or 4D visualization; (3) distribution of images processing; (4) segmentation of images or (5) registration of images; (6) filtering of images.
Allows users to perform 2D and 3D non-rigid image registration. MIRT is a standalone software which includes six main features for completing: (i) similarity measures such as residual complexity (RC) or Correlation Coefficient (CC), (ii) transformation models both parametric and non-parametric, (iii) optimization, (iv) regularization, (v) a hierarchical registration and (vi) groupwise registration.
Offers a digital imaging and communications in medicine (DICOM) solution. OsiriX is an image processing software that provides displaying, reviewing, interpreting and post-processing image files. It supports DICOM standard for a complete integration in a workflow environment and in a picture archiving and communication system (PACS).
Provides users a medical imaging file format and Toolbox for use in medical imaging. The original MINC file format and tools were based upon the NetCDF data format. The actual version was changed to HDF in order to support large files and other new features.
Performs image segmentation and registration. CMP-BIA is dedicated to ImageJ/Fiji and contains a plugin named jSLIC. This plugin is a segmentation method for clustering, in a given image, similar regions (as known as superpixels) which are usually used for other segmentation techniques, classification and registration. It gives reliable superpixels shapes, with no need of decreasing their size.
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.
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).
Allows to work on neonatal brain Magnetic Resonance (MR) image, including rigid, affine, and non-rigid transformations. MIRTK consists in a command line tool and a collection of libraries allowing to analyze and process imaging data. The software can be used for reconstruction of cortical surface meshes.
A set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison.
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