8000 [ENH]: Add functions to mrtrix3 interface by lbutry · Pull Request #3613 · nipy/nipype · GitHub
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[ENH]: Add functions to mrtrix3 interface #3613

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Merged
merged 19 commits into from
Mar 20, 2024
Merged

[ENH]: Add functions to mrtrix3 interface #3613

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984b7e8
added node maskfilter
Oct 17, 2023
a1ea55a
fixed comma
Oct 17, 2023
fa70f4a
fixed _list_outputs
Oct 17, 2023
a5afb28
added url to mrtrix3 docu
Oct 17, 2023
a9161e2
added mtnormalise
Oct 23, 2023
4f04c14
added mtnormalise
Oct 23, 2023
25e8ec6
fixing mtnormalise
Oct 23, 2023
bb3d352
fixed: renaming
Oct 23, 2023
820d1c3
fixed output of mtnormalise
Oct 24, 2023
c16cb34
fixing mtnormalise
Oct 24, 2023
20c0995
added 5ttgmwmi
Oct 24, 2023
a26c6b1
fixed comma
Oct 24, 2023
bc595b8
adding my name
Oct 24, 2023
bff1028
Merge branch 'master' into added_mrtrix3_functions
effigies Mar 17, 2024
27d285a
Update nipype/interfaces/mrtrix3/utils.py
effigies Mar 17, 2024
9720b95
MNT: Run codespell and black
effigies Mar 20, 2024
903dee5
TEST: make specs
effigies Mar 20, 2024
8c9c041
DOCTEST: Resolve typos
effigies Mar 20, 2024
5599348
TEST: Fix doctests, add example file stubs
effigies Mar 20, 2024
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added node maskfilter
  • Loading branch information
Lionel Butry committed Oct 17, 2023
commit 984b7e8c34c33aed7d2272f476f03d9f3dc8b90e
1 change: 1 addition & 0 deletions nipype/interfaces/mrtrix3/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,5 @@
SHConv,
TensorMetrics,
TransformFSLConvert,
MaskFilter,
)
61 changes: 61 additions & 0 deletions nipype/interfaces/mrtrix3/utils.py
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Expand Up @@ -1186,3 +1186,64 @@ def _list_outputs(self):
outputs = self.output_spec().get()
outputs["out_file"] = op.abspath(self.inputs.out_file)
return outputs

class MaskFilterInputSpec(CommandLineInputSpec):
in_file = File(
exists=True,
mandatory=True,
argstr="%s",
position=-3,
desc="Input mask",
)
filter = traits.Str(
mandatory=True,
argstr="%s",
position=-2,
desc="Filter to perform (e.g. dilate, erode)"
)
out_file = File(
name_source=["input_image"],
mandatory=True,
argstr="%s",
position=-1
desc="Output mask"
)
npass = traits.Int(
argstr="-npass %d",
position=1,
desc="Number of passes"
)

class MaskFilterOutputSpec(TraitedSpec):
out_file = File(exists=True, desc="the filtered output mask")

class MaskFilter(CommandLine):
"""
Perform filtering operations on 3D / 4D mask images.
Only supports dilate / erode filters at the moment.


Example
-------

>>> import nipype.interfaces.mrtrix3 as mrt
>>> mf = mrt.MaskFilter()
>>> mf.inputs.in_file = 'mask.mif'
>>> mf.inputs.filter = 'dilate'
>>> mf.inputs.npass = 2
>>> mf.out_file = 'mask_filtered.mif'
>>> mf.cmdline
'maskfilter -npass 2 mask.mif dilate mask_filtered.mif'
>>> mf.run()
"""

_cmd = "maskfilter"
input_spec = MaskFilterInputSpec
output_spec = MaskFilterOutputSpec

def _list_outputs(self):
outputs = self.output_spec().get()
outputs = self.output_spec().get()
inputs = self.input_spec().get()
outputs["output_image"] = self._gen_filename(inputs["input_image"], suffix="_filtered")
return outputs
0