diff --git a/samseg/SamsegLongitudinal.py b/samseg/SamsegLongitudinal.py
index f4ed2f1..282cd6a 100644
--- a/samseg/SamsegLongitudinal.py
+++ b/samseg/SamsegLongitudinal.py
@@ -855,12 +855,12 @@ def generateSubjectSpecificTemplate(self, saveWarp=False):
             # Read in the various time point images, and compute the average
             numberOfTimepoints = len(contrastImageFileNames)
             image0 = sf.load_volume(contrastImageFileNames[0])
-            imageBuffer = image0.transform(sf.Affine(self.tpToBaseTransforms[0]))
+            imageBuffer = image0.transform(self.tpToBaseTransforms[0])
             # Make sure that we are averaging only non zero voxels
             count = np.zeros(imageBuffer.shape)
             count[imageBuffer > 0] += 1
             for timepointNumber in range(1, numberOfTimepoints):
-                tmp = sf.load_volume(contrastImageFileNames[timepointNumber]).transform(sf.Affine(self.tpToBaseTransforms[timepointNumber])).data
+                tmp = sf.load_volume(contrastImageFileNames[timepointNumber]).transform(self.tpToBaseTransforms[timepointNumber]).data
                 imageBuffer += tmp
                 count[tmp > 0] += 1
             # Make sure that we are not dividing by zero for, e.g., background voxels
diff --git a/samseg/cli/run_samseg_long.py b/samseg/cli/run_samseg_long.py
index 1748e63..e9f1cf3 100644
--- a/samseg/cli/run_samseg_long.py
+++ b/samseg/cli/run_samseg_long.py
@@ -169,7 +169,8 @@ def check_lta_file(filepath):
     else:
         print("Assuming an identity transformation between base and each time point")
         for tp in args.timepoint:
-            tpToBaseTransforms.append(sf.Affine(np.eye(4)))
+            tpVol = sf.load_volume(tp)
+            tpToBaseTransforms.append(sf.Affine(np.eye(4), source=tpVol.geom, target=tpVol.geom))
 
 
     # ------ Run Samsegment ------