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.

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.