October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow

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

1. Prepare the data using the instructions -- LINK
2. Gradient anisotropic diffusion -- (time step: 0.0625, iterations: 5)
3. BRAINSFit initial registration -- PARAMETERS -- failure to recover the pose for Hugo and Valentino (both have severe head tilt in all three planes)
4. Manual pose alignment for Hugo and Valentino
5. Manual ICC for Tommy (Ginger, itkSNAP)
6. Manual ICC label map smoothed using slicer smoothing label map model -( 10 iterations).
7. Manual mask dilate for initial skull striping of other objects --(8-neighbours, 3 times).
8. Resampling of the ICC to each subject
9. Bias field correction with ICC
10. Pipelined registration -- problems with ICC, resampling the transform