Difference between revisions of "October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflow"
From NAMIC Wiki
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# Manual ICC for Tommy (Ginger, itkSNAP) | # Manual ICC for Tommy (Ginger, itkSNAP) | ||
# Manual ICC label map smoothed using slicer smoothing label map model -( 10 iterations). | # Manual ICC label map smoothed using slicer smoothing label map model -( 10 iterations). | ||
| − | # Manual mask dilate for initial skull striping of other objects --(8- | + | # Manual mask dilate for initial skull striping of other objects --(8-neighbors, 3 times). |
# Resampling of the ICC to each subject | # Resampling of the ICC to each subject | ||
# Bias field correction with ICC | # Bias field correction with ICC | ||
# Pipelined registration -- problems with ICC, resampling the transform | # Pipelined registration -- problems with ICC, resampling the transform | ||
Revision as of 02:17, 9 October 2009
Home < October 08 2009 Meeting: VT-NAMIC Revised atlas construction workflowTODOs
- 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)
- Manual ICC label map smoothed using slicer smoothing label map model -( 10 iterations).
- Manual mask dilate for initial skull striping of other objects --(8-neighbors, 3 times).
- Resampling of the ICC to each subject
- Bias field correction with ICC
- Pipelined registration -- problems with ICC, resampling the transform
