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made config option optional #31

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Merged
merged 1 commit into from
Sep 11, 2025
Merged

made config option optional #31

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4 changes: 2 additions & 2 deletions pydra/tasks/mrtrix3/manual/mrcalc.py
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Expand Up @@ -62,7 +62,7 @@ class MrCalcOp(Enum):


def operations_formatter(
operations: ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]]
operations: ty.List[ty.Tuple[ty.List[ty.Union[ImageIn, float]], MrCalcOp]],
):
return " ".join(
[
Expand Down Expand Up @@ -272,7 +272,7 @@ class MrCalc(shell.Task["MrCalc.Outputs"]):
default=None,
)

config: MultiInputObj[tuple[str, str]] = shell.arg(
config: MultiInputObj[tuple[str, str]] | None = shell.arg(
argstr="-config",
help="""temporarily set the value of an MRtrix config file entry.""",
)
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_3dautomask.py
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Expand Up @@ -154,7 +154,7 @@ class Dwi2Mask_3dautomask(shell.Task["Dwi2Mask_3dautomask.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_ants.py
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Expand Up @@ -104,7 +104,7 @@ class Dwi2Mask_Ants(shell.Task["Dwi2Mask_Ants.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_b02template.py
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Expand Up @@ -127,7 +127,7 @@ class Dwi2Mask_B02template(shell.Task["Dwi2Mask_B02template.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_consensus.py
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Expand Up @@ -112,7 +112,7 @@ class Dwi2Mask_Consensus(shell.Task["Dwi2Mask_Consensus.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_fslbet.py
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Expand Up @@ -124,7 +124,7 @@ class Dwi2Mask_Fslbet(shell.Task["Dwi2Mask_Fslbet.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_hdbet.py
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Expand Up @@ -104,7 +104,7 @@ class Dwi2Mask_Hdbet(shell.Task["Dwi2Mask_Hdbet.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_legacy.py
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Expand Up @@ -97,7 +97,7 @@ class Dwi2Mask_Legacy(shell.Task["Dwi2Mask_Legacy.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_mean.py
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Expand Up @@ -107,7 +107,7 @@ class Dwi2Mask_Mean(shell.Task["Dwi2Mask_Mean.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_mtnorm.py
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Expand Up @@ -116,7 +116,7 @@ class Dwi2Mask_Mtnorm(shell.Task["Dwi2Mask_Mtnorm.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_synthstrip.py
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Expand Up @@ -119,7 +119,7 @@ class Dwi2Mask_Synthstrip(shell.Task["Dwi2Mask_Synthstrip.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2mask_trace.py
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Expand Up @@ -117,7 +117,7 @@ class Dwi2Mask_Trace(shell.Task["Dwi2Mask_Trace.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_dhollander.py
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Expand Up @@ -147,7 +147,7 @@ class Dwi2Response_Dhollander(shell.Task["Dwi2Response_Dhollander.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_fa.py
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Expand Up @@ -129,7 +129,7 @@ class Dwi2Response_Fa(shell.Task["Dwi2Response_Fa.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_manual.py
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Expand Up @@ -122,7 +122,7 @@ class Dwi2Response_Manual(shell.Task["Dwi2Response_Manual.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_msmt_5tt.py
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Expand Up @@ -145,7 +145,7 @@ class Dwi2Response_Msmt_5tt(shell.Task["Dwi2Response_Msmt_5tt.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_tax.py
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Expand Up @@ -129,7 +129,7 @@ class Dwi2Response_Tax(shell.Task["Dwi2Response_Tax.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwi2response_tournier.py
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Expand Up @@ -134,7 +134,7 @@ class Dwi2Response_Tournier(shell.Task["Dwi2Response_Tournier.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwibiascorrect_ants.py
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Expand Up @@ -119,7 +119,7 @@ class DwiBiascorrect_Ants(shell.Task["DwiBiascorrect_Ants.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwibiascorrect_fsl.py
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Expand Up @@ -106,7 +106,7 @@ class DwiBiascorrect_Fsl(shell.Task["DwiBiascorrect_Fsl.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwibiascorrect_mtnorm.py
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Expand Up @@ -113,7 +113,7 @@ class DwiBiascorrect_Mtnorm(shell.Task["DwiBiascorrect_Mtnorm.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwibiasnormmask.py
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Expand Up @@ -143,7 +143,7 @@ class DwiBiasnormmask(shell.Task["DwiBiasnormmask.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwicat.py
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Expand Up @@ -87,7 +87,7 @@ class DwiCat(shell.Task["DwiCat.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwifslpreproc.py
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Expand Up @@ -192,7 +192,7 @@ class DwiFslpreproc(shell.Task["DwiFslpreproc.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwigradcheck.py
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Expand Up @@ -105,7 +105,7 @@ class DwiGradcheck(shell.Task["DwiGradcheck.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwinormalise_group.py
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Expand Up @@ -92,7 +92,7 @@ class DwiNormalise_Group(shell.Task["DwiNormalise_Group.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwinormalise_manual.py
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Expand Up @@ -102,7 +102,7 @@ class DwiNormalise_Manual(shell.Task["DwiNormalise_Manual.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwinormalise_mtnorm.py
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Expand Up @@ -120,7 +120,7 @@ class DwiNormalise_Mtnorm(shell.Task["DwiNormalise_Mtnorm.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/dwishellmath.py
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Expand Up @@ -116,7 +116,7 @@ class DwiShellmath(shell.Task["DwiShellmath.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/fivettgen_deep_atropos.py
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Expand Up @@ -101,7 +101,7 @@ class FivettGen_Deep_atropos(shell.Task["FivettGen_Deep_atropos.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/fivettgen_freesurfer.py
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Expand Up @@ -104,7 +104,7 @@ class FivettGen_Freesurfer(shell.Task["FivettGen_Freesurfer.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/fivettgen_fsl.py
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Expand Up @@ -122,7 +122,7 @@ class FivettGen_Fsl(shell.Task["FivettGen_Fsl.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/fivettgen_gif.py
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Expand Up @@ -99,7 +99,7 @@ class FivettGen_Gif(shell.Task["FivettGen_Gif.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/fivettgen_hsvs.py
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Expand Up @@ -117,7 +117,7 @@ class FivettGen_Hsvs(shell.Task["FivettGen_Hsvs.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/labelsgmfirst.py
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Expand Up @@ -103,7 +103,7 @@ class LabelSgmfirst(shell.Task["LabelSgmfirst.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/mask2glass.py
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Expand Up @@ -87,7 +87,7 @@ class Mask2Glass(shell.Task["Mask2Glass.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/mrtrix_cleanup.py
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Expand Up @@ -87,7 +87,7 @@ class MrTrix_Cleanup(shell.Task["MrTrix_Cleanup.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/population_template.py
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Expand Up @@ -250,7 +250,7 @@ class PopulationTemplate(shell.Task["PopulationTemplate.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down
2 changes: 1 addition & 1 deletion pydra/tasks/mrtrix3/v3_1/responsemean.py
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Expand Up @@ -87,7 +87,7 @@ class ResponseMean(shell.Task["ResponseMean.Outputs"]):
argstr="-nthreads",
default=None,
)
config: MultiInputObj[MultiInputObj] = shell.arg(
config: MultiInputObj[MultiInputObj] | None = shell.arg(
help="temporarily set the value of an MRtrix config file entry.",
argstr="-config",
default=None,
Expand Down