2011 Summer Project Week Breakout Session EMRegistration

Summer Project Week Breakout Session: Registration for EM Segmenter

Wednesday, June 22, 2011, 3-4pm, Star room.

Synopsis:

The EM segmenter includes as a vital step the co-registration of a multiple subject atlas to obtain spatial priors for small region detection. The success of these priors depends heavily on the quality of the registration obtained. Because the registration includes a large-DOF nonrigid inter-subject registration, benchmarks for a good solution are largely absent. We seek an implementation of a registration using Slicer registration tools that will provide best possible robustness and if possible an estimate of reliability. Because this registration will be integrated into a slicer module, tools with a BSD license are strongly preferred.

Attendees

• Kilian Pohl
• Dominik Meier
• Dominique Belhachemi
• Greg Sharp
• Danielle Pace
• Hans Johnson
• Jim Miller
• Daniel Haehn

Reference Material:

• Example case of 2 brains to register (.zip file, 16MB)

Preliminary Agenda:

• Description of the registration task for the EM segmenter
• Review of example case
• Comparison of BRAINSfit and CMTK strategies
• Discussion of design/implementation options/strategies

Meeting Notes:

• Hans pointed out that an upcoming fix, soon to be in ITK4, will incorporate an improved placement of control points, which reduces the need for masking
• the multiresolution approach and fine & adaptive grid are likely the reason for the good performance of CMTK on inter-subject registration
• CMTK takes ~1hr and does not have a BSD license, bootstrapping of transforms for saving time require transform concatenation
• skull stripped masks are not necessarily avail. for all use cases and should not be expected as avail. input
• emulation of CMTK behavior would require concatenation of multiple nonrigid transforms, which is also forthcoming in ITK4
• Alternatives:
  • Plastimatch was not designed for brain MRI, but it does have multiresolution
  • 2 track approach, using multiple versions that use different registration methods
  • NA-MIC sandbox options: Andryi
  • Nonrigid registration within the ANTS package