NA-MIC WFU VT Collaboration: Segmentation workflow and approaches

Segmentation workflow

1. Deformable registration of the atlas to the subject to be segmented
2. Segmentation using one of the approaches below

For State 1 scans, the workflow is the following:

1. Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
2. Map the Baseline ICC mask to the State 1 space
3. Skull stripping State 1 scan
4. Bias-correction of State 1 scan
5. 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)