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 for instance skull stripping, image registration, subcortical segmentation, cortical surface reconstruction, cortical segmentation, cortical thickness estimation, longitudinal processing, fMRI analysis or tractography.
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.
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.
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).
Offers a platform for investigating preclinical magnetic resonance imaging (MRI). ParaVision consists of a set of functions including automated acquisition and processing, real-time optimization during scanning, on-the-fly radiofrequence (RF)-pulse calculation as well as features for image reconstruction. It also be customized with several optional packages encompassing the fields of animal MRI or spectroscopy applications.
Allows to visualize, process, and integrate with anatomical magnetic resonance imaging (MRI) data, magnetoencephalography (MEG) and electroencephalography (EEG) data. Brainstorm aims to provide a set of tools to the scientific community using MEG/EEG as an experimental technique. User can interact with MEG/EEG recordings including various displays of time series, topographical mapping on 2D or 3D surfaces, generation of animations and series of snapshots of identical viewpoints at sequential time points, the selection of channels and time segments, and the manipulation of clusters of sensors.