--- a
+++ b/R/jacobian_lung.R
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+#' Calculate Jacobian Determinant Image for the Lungs
+#'
+#' This function calculates the Jacobian determinant image for the left and right lungs separately.
+#'
+#' @param right_transformation Transformations for the right lung
+#' @param left_transformation Transformations for the left lung
+#' @param mask Fixed mask (or standard lung template mask)
+#' @param doLog Return the log Jacobian
+#' @param geom Use the geometric Jacobian calculation
+#' @param relative Returen the relative Jacobian (Jacobian divided by mean Jacobian)
+#'
+#' @return Jacobian Image
+#' @importFrom ANTsR createJacobianDeterminantImage maskImage
+#'
+#' @export
+jacobian_lung = function(
+  right_transformation,
+  left_transformation,
+  mask,
+  doLog = TRUE,
+  geom = FALSE,
+  relative = TRUE
+) {
+
+  # Create separate left and right masks
+  right = mask == 1
+  left = mask == 2
+
+  # Create Jacobian Determinant Image
+  jacob_right <- createJacobianDeterminantImage(domainImg = mask,
+                                          tx = right_transformation,
+                                          doLog = doLog,
+                                          geom = FALSE)
+  jacob_right <- maskImage(jacob_right, right)
+
+  jacob_left <- createJacobianDeterminantImage(domainImg = mask,
+                                                tx = left_transformation,
+                                                doLog = doLog,
+                                                geom = FALSE)
+  jacob_left <- maskImage(jacob_left, left)
+
+  # Put images together
+  jacob = jacob_right + jacob_left
+
+  if(relative){
+
+    jacob_right_relative <- jacob_right/mean(jacob_right)
+    jacob_left_relative <- jacob_left/mean(jacob_left)
+    jacob_relative <- jacob_right_relative + jacob_left_relative
+
+    mylist = list(jacob = jacob,
+                  jacob_relative = jacob_relative)
+  }else{
+    mylist = jacob
+  }
+
+  return(mylist)
+}
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