- Run the graph cut segmentation on the WBCT scan
- Downsample WBCT image to DYNACT volume #1 spacing
- Reorient WBCT image to DYNACT volume #1 orientation (should be LAS)
- Initialize registration using ITK-SNAP (manual alignment in the registration function)
- Make sure to save the transform for the initialization as a text file
- Run the registration
- Optional step: in the case that the segmentation doesn't align with the grayscale image after reorientation, resample the segmentation image to match the grayscale image spacing, origin, etc. Then proceed with the workflow.
- Reorient the WBCT segmentation image to the DYNACT volume #1 orientation
- Transform the segmentation to the DYNACT volume #1 image
- Run the sequential registration
- Compute metrics