Research > Software > BSE

Brain Surface Extractor

Brain Surface Extraction: Designed to automatically extract the brain from a set of T1 weighted Magnetic Resonance (MR) images of the human head.



Features

  • The user can either run the command-line version, specifying parameter values ahead of time, or use the interactive X-Windows based version, which allows the user to interactively monitor the extraction process and alter extraction parameters during the process. In general, the user should only have to specify one input parameter (if pre-filtering of the MR volume is not required) or three input parameters (if pre-filtering is specified). Obtaining the best results requires some degree of trial and error in selecting these parameters, but this can be done rapidly by initially processing only 10-20 slices of the data as discussed below.
  • The user is prompted for the input parameters, and possibly for details concerning the size and format of the input data. The user can also select among several output options, including the detailed brain volume (default name: brain.bin) which is a binary volume defining the extracted brain surface, and the smoothed brain volume (default name: mask.bin) which contains a binary volume defining the morphologically smoothed and filled brain.

Description

The distribution package for BSE contains two executables. The first is bse, a text based version of the software. The second is xbse an X/Motif based interactive GUI, which allows each step of the process to be viewed, and the parameters to be altered during the sequence. The degree of user interaction is variable; the either can either run the command-line version, specifying parameter values ahead of time, or use the interactive X-Windows based version, and move through the steps to determine appropriate values.

Purpose

The routines in BSE are designed to automatically extract the brain from a set of T1-weighted Magnetic Resonance (MR) images of the human head. The goal in developing this software was to find a procedure which extracts the brain from the skull, dura and other connective tissues and produces a brain volume whose boundary tracks the major sulci.