[FIX] Correct the pet-linear pipeline (#1348)

* Use T1W linear for non linear registration

* run precommit

* Update clinica/pipelines/pet/linear/pipeline.py

* Update clinica/pipelines/pet/linear/pipeline.py

---------

Co-authored-by: Gensollen <[email protected]>

clinica/pipelines/pet/linear/pipeline.py

@@ -38,7 +38,7 @@ def get_input_fields(self) -> List[str]:
         list of str :
             A list of (string) input fields name.
         """
-        return ["pet", "t1w", "t1w_to_mni"]
+        return ["pet", "t1w", "t1w_to_mni", "t1w_linear"]
 
     def get_output_fields(self) -> List[str]:
         """Specify the list of possible outputs of this pipeline.
@@ -66,7 +66,12 @@ def _build_input_node(self):
             ClinicaException,
         )
         from clinica.utils.image import get_mni_template
-        from clinica.utils.input_files import T1W_NII, T1W_TO_MNI_TRANSFORM
+        from clinica.utils.input_files import (
+            T1W_LINEAR,
+            T1W_LINEAR_CROPPED,
+            T1W_NII,
+            T1W_TO_MNI_TRANSFORM,
+        )
         from clinica.utils.inputs import clinica_file_reader
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
@@ -102,6 +107,21 @@ def _build_input_node(self):
             raise ClinicaBIDSError(err)
 
         # Inputs from t1-linear pipeline
+        # T1w images registered
+        t1w_linear_file_pattern = (
+            T1W_LINEAR
+            if self.parameters.get("uncropped_image", False)
+            else T1W_LINEAR_CROPPED
+        )
+        try:
+            t1w_linear_files, _ = clinica_file_reader(
+                self.subjects,
+                self.sessions,
+                self.caps_directory,
+                t1w_linear_file_pattern,
+            )
+        except ClinicaException as e:
+            raise ClinicaCAPSError(e)
         # Transformation files from T1w files to MNI:
         try:
             t1w_to_mni_transformation_files, _ = clinica_file_reader(
@@ -124,6 +144,7 @@ def _build_input_node(self):
                 ("t1w", t1w_files),
                 ("pet", pet_files),
                 ("t1w_to_mni", t1w_to_mni_transformation_files),
+                ("t1w_linear", t1w_linear_files),
             ],
             synchronize=True,
             interface=nutil.IdentityInterface(fields=self.get_input_fields()),
@@ -133,6 +154,7 @@ def _build_input_node(self):
                 (read_input_node, self.input_node, [("t1w", "t1w")]),
                 (read_input_node, self.input_node, [("pet", "pet")]),
                 (read_input_node, self.input_node, [("t1w_to_mni", "t1w_to_mni")]),
+                (read_input_node, self.input_node, [("t1w_linear", "t1w_linear")]),
             ]
         )
 
@@ -394,12 +416,12 @@ def _build_core_nodes(self):
                 (
                     self.input_node,
                     ants_registration_nonlinear_node,
-                    [("t1w", "moving_image")],
+                    [("t1w_linear", "moving_image")],
                 ),
                 (
                     ants_registration_nonlinear_node,
                     ants_applytransform_nonlinear_node,
-                    [("reverse_forward_transforms", "transforms")],
+                    [("forward_transforms", "transforms")],
                 ),
                 (
                     ants_applytransform_node,