Smoothing multi-label brain segmentations
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smoothing workflow
- Deformable registration of the atlas to the subject to be segmented
- Segmentation using one of the approaches below
For State 1 scans, the workflow is the following:
- Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
- Map the Baseline ICC mask to the State 1 space
- Skull stripping State 1 scan
- Bias-correction of State 1 scan
- Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline
Considered segmentation approaches
Choice of atlas:
- Vervet atlas
- Rhesus atlas
Choice of segmentation approach:
- fluid deformable registration of a specific atlas to the subject (UNC approach)
- EM Segmenter (Kilian Pohl)
- itkEMS/ABC (Marcel Prastawa)