Research > Software > BrainParser
Brain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retrained to work with your desired regions of interest.Visit BrainParser Forum
DescriptionBrain Parser software segments regions of interest based on a training set of data and generates 3D MRI volumes. The software comes pre-trained on a provided data set but can be retained to work with your desired regions of interest. Brain Parser specifically includes skull and scalp removal, image nonuniformity compensation, voxel-based tissue classification, topological correction, rendering, and editing functions. The collection of tools is designed to require minimal user interaction to produce cortical representations. Surface representations of the human cerebral cortex are important for visualization and analysis of neuroimaging data (Thompson et al., 1997) and as constraints for localizing functional activation from magneto-encephalography (MEG) and electro-encephalography (EEG) data (Dale and Baillet). MR imaging offers neuroanatomical detail, but extraction of cortical surfaces from MR imagery faces several problems, including measurement noise, partial volume effects, and image nonuniformity do to magnetic field inhomogeneities.
The following steps are required to go from raw data to fully segmented data: <ul> <li>Data must be in Analyze Image 16 bit short format and should have a reasonable intensity range from 0 to 5000</li> <li>Data must be aligned to the template image</li> <li>Skull stripping</li> <li>Registration</li> <li>Intensity normalization</li> <li>After you run LONI Brain Parser you will need to invert your registration to match the orientation of the original data</li> </ul> If you have good quality data that approximates the template image, your results are likely to be more successful.<br /> <br /> Alternatively, you can run the LONI Brain Parser-Pipeline Workflow in our <a target=\"_blank\" href=\"demo.php?id=69\">Try it now</a> area. The workflow has been setup with the pre-processing and post-processing steps predefined for ease of use.
LONI Brain Parser allows the user to quickly segment anatomical brain structures using automated delineation methods. The software can also be "trained" to locate areas of interest in the brain that it is not programmed to locate by default. Whereas segmentation by hand can take hours or even days, auto-segmentation only takes about half an hour. With this segmented data researchers can study the shape and morphometry of the structures to discover new patterns and associations in areas such as development and disease.