diff --git a/nipype/interfaces/mrtrix/preprocess.py b/nipype/interfaces/mrtrix/preprocess.py index 48f4bde719..495f3af703 100644 --- a/nipype/interfaces/mrtrix/preprocess.py +++ b/nipype/interfaces/mrtrix/preprocess.py @@ -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, @@ -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, + 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, diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 25bae449e3..72a2820cc1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -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, diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index c1e91da1c1..f619525575 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -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,