Hi All,
Hoping to find help with strategies in registering a time series of abdomen images. Respiratory motion is a bit tricky since all organs don't move exactly uniformly. I'm mostly interested in registering just one organ. So willing to use a mask with the base image but wasn't sure how to do that in 3dAllineate. I tried '-source_mask' but it completely threw off the registration (much worse than without). Below is what I previously tried.
# 2D REGISTER
3dAllineate \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.Reg \
-base $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig[0] \
-warp shift_only \
-parfix 3 0 \
$AnimalID/$FolderID/${AnimalID}_${FolderID}+orig
Any help to improve the registration is greatly appreciated. Thank you!
Edwin
