2011 Summer Project Week Registration of mouse brains

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Registration of mouse brain

Key Investigators

• UNC NIRAL: Francois Budin, Ipek Oguz, Martin Styner
• BWH: Dominik Meier

Objective

Registration of mouse brain images is really hard to achieve properly with certain types of images (in particular T1).Indeed, the size of those images is very different from the size of human brain images. The ratio of rotation, translation and scaling in the transformations is going to be very different in both case. Most modules included in Slicer have default parameters set up for human images. The goal of this project is to provide a framework that is adapted to register easily and automatically mouse brain images in Slicer.

Approach, Plan

During the NAMIC project week, I will try to run the different registration modules available in Slicer to figure out some good sets of parameters that allow good mouse brain registrations. This results will be integrated in DWIProcessPipeline, a module for Slicer that will compute a DTI from a DWI image, register a scalar image computed from the DTI to a template and then computes scalar images from the registered DTI.

• Usecase #3 in the BRAINSFit documentation demonstrates mouse brain registration using BRAINSFit.

Progress

Delivery Mechanism

This work will be delivered to the NAMIC Kit as a

1. NITRIC distribution
2. Slicer Module