October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow
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TODOs
- link the software tools and scripts with the workflow
- prepare a branch in the sandbox with the tools not available in Slicer (confirm with Chris copyright issues)
Software
- Slicer/extensions versioning
Workflow
- Prepare the data using the instructions -- LINK
- Gradient anisotropic diffusion -- (time step: 0.0625, iterations: 5)
- BRAINSFit initial registration -- PARAMETERS -- failure to recover the pose for Hugo and Valentino (both have severe head tilt in all three planes)
- Manual pose alignment for Hugo and Valentino
- Manual ICC for Tommy (Ginger, itkSNAP)
- Resampling of the ICC to each subject
- Bias field correction with ICC
- Pipelined registration -- problems with ICC, resampling the transform