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.

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).

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.

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.

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.