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[ENH] pet-volume class ApplySegmentationDeformation should inherit from Nipype ApplyDeformations #1548

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[ENH] pet-volume class ApplySegmentationDeformation should inherit from Nipype ApplyDeformations #1548

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c61438a
Proposition
AliceJoubert Sep 17, 2025
5bd9156
Use integrated type list
AliceJoubert Sep 17, 2025
7217594
Use integrated types in utils
AliceJoubert Sep 17, 2025
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23 changes: 3 additions & 20 deletions clinica/pipelines/t1_volume_tissue_segmentation/t1_volume_tissue_segmentation_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,10 @@
from nipype.interfaces.base import (
File,
InputMultiPath,
OutputMultiPath,
TraitedSpec,
traits,
)
from nipype.interfaces.spm.base import SPMCommand, SPMCommandInputSpec
from nipype.interfaces.spm.base import SPMCommandInputSpec
from nipype.interfaces.spm.preprocess import ApplyDeformations
from nipype.utils.filemanip import filename_to_list, list_to_filename


Expand Down Expand Up @@ -129,11 +128,7 @@ class ApplySegmentationDeformationInput(SPMCommandInputSpec):
)


class ApplySegmentationDeformationOutput(TraitedSpec):
out_files = OutputMultiPath(File(exists=True), desc="Transformed files")


class ApplySegmentationDeformation(SPMCommand):
class ApplySegmentationDeformation(ApplyDeformations):
"""Uses SPM to apply a deformation field obtained from Segmentation routine to a given file

Examples
Expand All @@ -147,10 +142,6 @@ class ApplySegmentationDeformation(SPMCommand):
"""

input_spec = ApplySegmentationDeformationInput
output_spec = ApplySegmentationDeformationOutput

_jobtype = "util"
_jobname = "defs"

def _format_arg(self, opt, spec, val):
"""Convert input to appropriate format for spm"""
Expand All @@ -159,11 +150,3 @@ def _format_arg(self, opt, spec, val):
if opt == "in_files":
return np.array(filename_to_list(val), dtype=object)
return val

def _list_outputs(self):
outputs = self._outputs().get()
outputs["out_files"] = []
for filename in self.inputs.in_files:
_, fname = os.path.split(filename)
outputs["out_files"].append(os.path.realpath("w%s" % fname))
return outputs
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