Advanced Segmentation Tools
Completion of BrainVoyager QX 1.7 took somewhat longer than expected. The reason was that I decided to make a number of important additions and changes to allow performing high-quality segmentations of both the white / grey matter (WM-GM) boundary as well as the grey matter / cerebrospinal fluid (GM-CSF) boundary. In addition, I also decided to finish the documentation for the new tools before releasing this substantial update. The updated documentation describes standard and advanced cortex segmentation and cortical thickness measurement tools and is available as part of the User’s Guide 0.8. As usual, the release notes list a number of other important new features, improvements and bug fixes.
The goal of the advanced segmentation tools is to provide highly accurate representations of the WM-GM as well as the GM-CSF boundary so that they are suitable for measuring cortical thickness in individual brains as precisely as possible. The figure on top of this blog entry shows a surface rendering on the outer cortex boundary (GM-CSF) obtained with the new segmentation tools.
The implemented Laplace method for cortical thickness measurements requires the determination of the WM-GM and GM-CSF boundaries in volume space. The standard segmentation tools provide only a single segmentation result with a voxel border running roughly one millimeter inside grey matter because of a performed dilation process. The dilation step is performed to help obtaining a topologically correct surface. It turned out to be difficult to accurately segment the WM-GM and the GM-CSF boundary using data sets with a resolution of 1 mm. One important difference between the advanced and standard segmentation tools is that the advanced tools work on a 0.5 mm resolution. This resolution is also better suited to measure cortical thickness with the Laplace method than a standard resolution of 1 mm. Note that the support for 0.5 mm resolution VMRs lead also to a new VMR file version and many changes in the internal operation of the program.
Another important new feature of the advanced segmentation tools is that intensity thresholds for segmentation of WM, GM and CSF are calculated adaptively by inspecting local intensity histograms as well as computed gradient fields. Note that the quality of the data submitted to the advanced segmentation tools should be very high, otherwise erroneous WM and GM segmentations might result.
The advanced segmentation tools are available in the Advanced Segmentation Tools dialog (see snapshot above), which is accessed from the new Volumes file menu.