diff --git a/hippunfold/workflow/rules/autotop.smk b/hippunfold/workflow/rules/autotop.smk
index 3d884a2c..3920bec8 100644
--- a/hippunfold/workflow/rules/autotop.smk
+++ b/hippunfold/workflow/rules/autotop.smk
@@ -231,6 +231,7 @@ rule unflip_coords:
             hemi="{hemi}flip",
             **config["subj_wildcards"]
         ),
+        unflip_ref=get_nnunet_input,
     output:
         nii=bids(
             root=work,
@@ -248,7 +249,8 @@ rule unflip_coords:
     group:
         "subj"
     shell:
-        "c3d {input} -flip x {output}"
+        "c3d {input.nii} -flip x -popas FLIPPED "
+        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nii} "
 
 
 rule unflip_coords_equivol:
@@ -264,6 +266,7 @@ rule unflip_coords_equivol:
             hemi="{hemi}flip",
             **config["subj_wildcards"]
         ),
+        unflip_ref=get_nnunet_input,
     output:
         nii=bids(
             root=work,
@@ -281,4 +284,5 @@ rule unflip_coords_equivol:
     group:
         "subj"
     shell:
-        "c3d {input} -flip x {output}"
+        "c3d {input.nii} -flip x -popas FLIPPED "
+        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nii} "
diff --git a/hippunfold/workflow/rules/nnunet.smk b/hippunfold/workflow/rules/nnunet.smk
index 98d9418b..9c00135f 100644
--- a/hippunfold/workflow/rules/nnunet.smk
+++ b/hippunfold/workflow/rules/nnunet.smk
@@ -158,6 +158,7 @@ rule unflip_nnunet_nii:
             space="corobl",
             hemi="{hemi}flip"
         ),
+        unflip_ref=get_nnunet_input,
     output:
         nnunet_seg=bids(
             root=work,
@@ -173,7 +174,8 @@ rule unflip_nnunet_nii:
     group:
         "subj"
     shell:
-        "c3d {input} -flip x {output}"
+        "c3d {input.nnunet_seg} -flip x -popas FLIPPED "
+        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nnunet_seg} "
 
 
 def get_f3d_ref(wildcards):
diff --git a/hippunfold/workflow/rules/shape_inject.smk b/hippunfold/workflow/rules/shape_inject.smk
index cc529e8e..c0d7318a 100644
--- a/hippunfold/workflow/rules/shape_inject.smk
+++ b/hippunfold/workflow/rules/shape_inject.smk
@@ -386,6 +386,7 @@ rule unflip_postproc:
             hemi="{hemi}flip",
             **config["subj_wildcards"]
         ),
+        unflip_ref=get_nnunet_input,
     output:
         nii=bids(
             root=work,
@@ -401,4 +402,5 @@ rule unflip_postproc:
     group:
         "subj"
     shell:
-        "c3d {input} -flip x {output}"
+        "c3d {input.nii} -flip x -popas FLIPPED "
+        " {input.unflip_ref} -push FLIPPED -copy-transform -o {output.nii} "