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Commit 6ac81ca

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Merge pull request #3658 from GalKepler/5ttgen
[ENH] Added available inputs for MRTrix3's 5ttgen
2 parents c5fa777 + 386dd14 commit 6ac81ca

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2 files changed

+74
-0
lines changed

2 files changed

+74
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lines changed

‎nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py‎

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@@ -28,6 +28,9 @@ def test_Generate5tt_inputs():
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argstr="-fslgrad %s %s",
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xor=["grad_file"],
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),
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hippocampi=dict(
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argstr="-hippocampi %s",
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),
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in_bval=dict(
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extensions=None,
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),
@@ -40,6 +43,17 @@ def test_Generate5tt_inputs():
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mandatory=True,
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position=-2,
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),
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lut_file=dict(
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argstr="-lut %s",
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extensions=None,
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),
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mask_file=dict(
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argstr="-mask %s",
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extensions=None,
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),
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nocrop=dict(
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argstr="-nocrop",
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),
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nthreads=dict(
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argstr="-nthreads %d",
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nohash=True,
@@ -57,6 +71,23 @@ def test_Generate5tt_inputs():
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mandatory=True,
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position=-1,
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),
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premasked=dict(
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argstr="-premasked",
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),
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sgm_amyg_hipp=dict(
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argstr="-sgm_amyg_hipp",
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),
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t2_image=dict(
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argstr="-t2 %s",
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extensions=None,
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),
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template=dict(
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argstr="-template %s",
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extensions=None,
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),
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white_stem=dict(
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argstr="-white_stem",
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),
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)
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inputs = Generate5tt.input_spec()
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‎nipype/interfaces/mrtrix3/utils.py‎

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Original file line numberDiff line numberDiff line change
@@ -241,6 +241,49 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
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desc="input image / directory",
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)
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out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")
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t2_image = File(
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exists=True,
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argstr="-t2 %s",
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desc="Provide a T2-weighted image in addition to the default T1-weighted image. (Only for 'fsl' algorithm)",
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)
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mask_file = File(
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exists=True,
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argstr="-mask %s",
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desc="Provide a brain mask image. (Only for 'fsl' algorithm)",
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)
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premasked = traits.Bool(
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argstr="-premasked",
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desc="Assume that the input image is already brain-masked. (Only for 'fsl' algorithm)",
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)
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nocrop = traits.Bool(
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argstr="-nocrop",
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desc="Do not crop the image to the region of interest.",
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)
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sgm_amyg_hipp = traits.Bool(
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argstr="-sgm_amyg_hipp",
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desc="Include the amygdala and hippocampus in the subcortical grey matter segment.",
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)
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template = File(
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exists=True,
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argstr="-template %s",
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desc="Provide an image that will form the template for the generated 5TT image. (Only for 'hsvs' algorithm)",
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)
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hippocampi = traits.Enum(
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"subfields",
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"first",
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"aseg",
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argstr="-hippocampi %s",
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desc="Choose the method used to segment the hippocampi. (Only for 'freesurfer' algorithm)",
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)
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white_stem = traits.Bool(
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argstr="-white_stem",
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desc="Classify the brainstem as white matter. (Only for 'hsvs' algorithm)",
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)
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lut_file = File(
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exists=True,
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argstr="-lut %s",
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desc="Manually provide path to the lookup table on which the input parcellation image is based. (Only for 'freesurfer' algorithm)",
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)
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class Generate5ttOutputSpec(TraitedSpec):

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