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ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) #3365

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Merged
merged 3 commits into from
Oct 13, 2021
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ENH: Add new flags to MRtrix/preprocess.py (DWI2Tensor, MRtransform) #3365

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6a84156
Add -mask flag to DWI2Tensor
alexandreroutier Aug 6, 2021
53dd0a4
Add -linear flag to MRTransform
alexandreroutier Aug 6, 2021
a1d56ab
Add tests from make check-before-commit
alexandreroutier Aug 8, 2021
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18 changes: 18 additions & 0 deletions nipype/interfaces/mrtrix/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,6 +217,13 @@ class DWI2TensorInputSpec(CommandLineInputSpec):
"specified when computing the tensor."
),
)
mask = File(
exists=True,
argstr="-mask %s",
desc=(
"Only perform computation within the specified binary brain mask image."
),
)
quiet = traits.Bool(
argstr="-quiet",
position=1,
Expand Down Expand Up @@ -865,6 +872,17 @@ class MRTransformInputSpec(CommandLineInputSpec):
position=1,
desc="Invert the specified transform before using it",
)
linear_transform = File(
exists=True,
argstr="-linear %s",
position=1,
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I'm confused as to why all of these are position=1, but I don't think it can hurt for another one to be.

desc=(
"Specify a linear transform to apply, in the form of a 3x4 or 4x4 ascii file. "
"Note the standard reverse convention is used, "
"where the transform maps points in the template image to the moving image. "
"Note that the reverse convention is still assumed even if no -template image is supplied."
),
)
replace_transform = traits.Bool(
argstr="-replace",
position=1,
Expand Down
4 changes: 4 additions & 0 deletions nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py
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Expand Up @@ -35,6 +35,10 @@ def test_DWI2Tensor_inputs():
mandatory=True,
position=-2,
),
mask=dict(
argstr="-mask %s",
extensions=None,
),
out_filename=dict(
argstr="%s",
extensions=None,
Expand Down
5 changes: 5 additions & 0 deletions nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py
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Expand Up @@ -28,6 +28,11 @@ def test_MRTransform_inputs():
argstr="-inverse",
position=1,
),
linear_transform=dict(
argstr="-linear %s",
extensions=None,
position=1,
),
out_filename=dict(
argstr="%s",
extensions=None,
Expand Down