BUG: Minor fixes.

Author: ntustison

ants/registration/registration.py

@@ -1738,7 +1738,8 @@ def label_image_registration(fixed_label_images,
                 count += 1
                 if do_deformable:
                     deformable_multivariate_extras.append(["MSQ", fixed_single_label_image, 
-                                                           moving_single_label_image, label_image_weighting, 0])
+                                                           moving_single_label_image, 
+                                                           label_image_weights[i], 0])
 
         linear_xfrm = ants.fit_transform_to_paired_points(moving_centers_of_mass, 
                                                           fixed_centers_of_mass, 
@@ -1793,7 +1794,7 @@ def label_image_registration(fixed_label_images,
                 intensity_metric = "CC"
                 if intensity_metric_parameter is None:
                     intensity_metric_parameter = 2
-            for i in range(1, len(fixed_intensity_images)):
+            for i in range(len(fixed_intensity_images)):
                 syn_stage.append("--metric")
                 metric_string = "%s[%s,%s,%s,%s]" % (
                     intensity_metric,
@@ -1808,7 +1809,7 @@ def label_image_registration(fixed_label_images,
                 "MSQ",
                 get_pointer_string(deformable_multivariate_extras[kk][1]),
                 get_pointer_string(deformable_multivariate_extras[kk][2]),
-                1.0, 0.0)
+                label_image_weights[kk], 0.0)
             syn_stage.append(metricString)     
 
         syn_shrink_factors = "8x4x2x1"
@@ -1832,9 +1833,14 @@ def label_image_registration(fixed_label_images,
             syn_stage.insert(0, "SyN[0.1,3,0]")
         syn_stage.insert(0, "--transform")
 
-        args = ["-d", str(image_dimension),
-                "-r", linear_xfrm_file,
-                "-o", output_prefix]
+        args = None
+        if linear_xfrm is None:
+          args = ["-d", str(image_dimension),
+                  "-o", output_prefix]
+        else:
+          args = ["-d", str(image_dimension),
+                  "-r", linear_xfrm_file,
+                  "-o", output_prefix]
         args.append(syn_stage)
 
         fixed_mask_string = 'NA' 
@@ -1884,14 +1890,15 @@ def label_image_registration(fixed_label_images,
     find_forward_warps = np.where([re.search("[0-9]Warp.nii.gz", ff) for ff in all_xfrms])[0]
 
     if len(find_inverse_warps) > 0:
-        fwdtransforms = list(reversed([ff for idx, ff in enumerate(all_xfrms) if idx != find_inverse_warps[0]]))
+        fwdtransforms = [find_forward_warps[0], linear_xfrm_file]
+        invtransforms = [linear_xfrm_file, find_inverse_warps[0]]
         invtransforms = [ff for idx, ff in enumerate(all_xfrms) if idx != find_forward_warps[0]]
     else:
         fwdtransforms = list(reversed(all_xfrms))
         invtransforms = all_xfrms
 
     if verbose:
-        print("\n\nResulting transforms:")
+        print("\n\nResulting transforms")
         print("  fwdtransforms: ", fwdtransforms)        
         print("  invtransforms: ", invtransforms)