8000 FIX: Check for non-mandatory output in DWIBiasCorrect by MatthieuJoulot · Pull Request #3523 · nipy/nipype · GitHub
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FIX: Check for non-mandatory output in DWIBiasCorrect #3523

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Merged
merged 3 commits into from
Oct 17, 2022
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FIX: Check for non-mandatory output in DWIBiasCorrect #3523

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07f4601
Fix non mandatory output issue in DWIBiasCorrect
MatthieuJoulot Sep 28, 2022
4b7993c
Fix indent level
MatthieuJoulot Sep 29, 2022
ddc81d3
Update nipype/interfaces/mrtrix3/preprocess.py
MatthieuJoulot Sep 29, 2022
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Fix non mandatory output issue in DWIBiasCorrect 
The function `_list_outputs` in `DWIBiasCorrect` doesn't take into account the fact that `output_file` is not a mandatory input, thus making any pipeline using this interface without specifying the output crash.
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@MatthieuJoulot
MatthieuJoulot authored Sep 28, 2022
commit 07f460168cdc52ca309cd7826e35ec416be05212
11 changes: 6 additions & 5 deletions nipype/interfaces/mrtrix3/preprocess.py
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Expand Up @@ -256,11 +256,12 @@ def _format_arg(self, name, trait_spec, value):
return super()._format_arg(name, trait_spec, value)

def _list_outputs(self):
outputs = self.output_spec().get()
outputs["out_file"] = op.abspath(self.inputs.out_file)
if self.inputs.bias:
outputs["bias"] = op.abspath(self.inputs.bias)
return outputs
if self.inputs.out_file:
outputs = self.output_spec().get()
outputs["out_file"] = op.abspath(self.inputs.out_file)
if self.inputs.bias:
outputs["bias"] = op.abspath(self.inputs.bias)
return outputs


class DWIPreprocInputSpec(MRTrix3BaseInputSpec):
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