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noticed that this error also happens for 'out_grad_fsl'. Fixed it
1 parent 6007848 commit f543c4a

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+16
-6
lines changed

1 file changed

+16
-6
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nipype/interfaces/mrtrix3/preprocess.py

+16-6
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,9 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
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mandatory=True,
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desc="input DWI image",
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)
195-
in_mask = File(argstr="-mask %s", desc="input mask image for bias field estimation")
195+
in_mask = File(
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argstr="-mask %s", desc="input mask image for bias field estimation"
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)
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use_ants = traits.Bool(
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argstr="ants",
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mandatory=True,
@@ -407,8 +409,10 @@ def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs["out_file"] = op.abspath(self.inputs.out_file)
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if self.inputs.out_grad_mrtrix:
410-
outputs["out_grad_mrtrix"] = op.abspath(self.inputs.out_grad_mrtrix)
411-
if self.inputs.export_grad_fsl:
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outputs["out_grad_mrtrix"] = op.abspath(
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self.inputs.out_grad_mrtrix
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)
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if self.inputs.out_fsl_bvec:
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outputs["out_fsl_bvec"] = op.abspath(self.inputs.out_grad_fsl[0])
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outputs["out_fsl_bval"] = op.abspath(self.inputs.out_grad_fsl[1])
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@@ -441,9 +445,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
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usedefault=True,
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desc="output WM response text file",
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)
444-
gm_file = File(argstr="%s", position=-2, desc="output GM response text file")
445-
csf_file = File(argstr="%s", position=-1, desc="output CSF response text file")
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in_mask = File(exists=True, argstr="-mask %s", desc="provide initial mask image")
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gm_file = File(
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argstr="%s", position=-2, desc="output GM response text file"
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)
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csf_file = File(
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argstr="%s", position=-1, desc="output CSF response text file"
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)
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in_mask = File(
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exists=True, argstr="-mask %s", desc="provide initial mask image"
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)
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max_sh = InputMultiObject(
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traits.Int,
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argstr="-lmax %s",

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