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Revert "[FIX] Correct the pet-linear pipeline (#1348)" #1357

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Oct 25, 2024
Merged

Revert "[FIX] Correct the pet-linear pipeline (#1348)" #1357

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30 changes: 4 additions & 26 deletions clinica/pipelines/pet/linear/pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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", "t1w_linear"]
return ["pet", "t1w", "t1w_to_mni"]

def get_output_fields(self) -> List[str]:
"""Specify the list of possible outputs of this pipeline.
Expand Down Expand Up @@ -66,12 +66,7 @@ def _build_input_node(self):
ClinicaException,
)
from clinica.utils.image import get_mni_template
from clinica.utils.input_files import (
T1W_LINEAR,
T1W_LINEAR_CROPPED,
T1W_NII,
T1W_TO_MNI_TRANSFORM,
)
from clinica.utils.input_files import 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
Expand Down Expand Up @@ -107,21 +102,6 @@ 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(
Expand All @@ -144,7 +124,6 @@ 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()),
Expand All @@ -154,7 +133,6 @@ 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")]),
]
)

Expand Down Expand Up @@ -416,12 +394,12 @@ def _build_core_nodes(self):
(
self.input_node,
ants_registration_nonlinear_node,
[("t1w_linear", "moving_image")],
[("t1w", "moving_image")],
),
(
ants_registration_nonlinear_node,
ants_applytransform_nonlinear_node,
[("forward_transforms", "transforms")],
[("reverse_forward_transforms", "transforms")],
),
(
ants_applytransform_node,
Expand Down
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