Solved by nmvr in post #3 
              
              
                Looking at the descriptions they provide for the transforms it doesn’t look to be what I needed. 
However, SimpleITK did have such a thing with the RegionOfInterest method which solved my problem. 
image_ct = sitk.ReadImage(path_ct, sitk.sitkInt16)
origin_indx = [zmin, xmin, ymin] #crop area start
s…