8000 [ENH]: Add functions to mrtrix3 interface by lbutry · Pull Request #3613 · nipy/nipype · GitHub
[go: up one dir, main page]
Skip to content

[ENH]: Add functions to mrtrix3 interface #3613

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 19 commits into from
Mar 20, 2024
Merged

[ENH]: Add functions to mrtrix3 interface #3613

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
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 < 10000 /div>
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
added 5ttgmwmi
  • Loading branch information
Lionel Butry committed Oct 24, 2023
commit 20c09951a5e681048c1608889427f01dd272ff51
1 change: 1 addition & 0 deletions nipype/interfaces/mrtrix3/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,4 +32,5 @@
TransformFSLConvert,
MaskFilter,
MTNormalise,
Generate5tt2gmwmi,
)
54 changes: 54 additions & 0 deletions nipype/interfaces/mrtrix3/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1331,4 +1331,58 @@ def _list_outputs(self):
outputs["out_file_wm"] = op.abspath(self.inputs.out_file_wm)
outputs["out_file_gm"] = op.abspath(self.inputs.out_file_gm)
outputs["out_file_csf"] = op.abspath(self.inputs.out_file_csf)
return outputs


class Generate5tt2gmwmiInputSpec(MRTrix3BaseInputSpec):
in_file = File(
exists=True,
argstr="%s",
mandatory=True,
position=-2,
desc="the input 5TT segmented anatomical image",
)
mask_out = File(
"mask_gmwmi.mif"
argstr="%s",
mandatory=True,
position=-1,
desc="the output mask image",
)
mask_in = File(
argstr="-mask_in %s",
position=-3,
desc="filter an imput mask image according to those voxels that lie upon the grey matter - white matter boundary",
)


class Generate5tt2gmwmiOutputSpec(TraitedSpec):
mask_out = File(exists=True, desc="the output mask file")


class Generate5tt2gmwmi(CommandLine):
"""
Generate a mask image appropriate for seeding streamlines on
the grey matter-white matter interface


Example
-------

>>> import nipype.interfaces.mrtrix3 as mrt
>>> gmwmi = mrt.Generate5TT2GMWMI()
>>> gmwmi.inputs.in_file = '5tt_in.mif'
>>> gmwmi.inputs.mask_out = 'mask_gmwmi.mif'
>>> gmwmi.cmdline
'5tt2gmwmi 5tt_in.mif mask_gmwmi.mif'
>>> gmwmi.run()
"""

_cmd = "5tt2gmwmi"
input_spec = Generate5tt2gmwmiInputSpec
output_spec = Generate5tt2gmwmiOutputSpec

def _list_outputs(self):
outputs = self.output_spec().get()
outputs["mask_out"] = op.abspath(self.inputs.mask_out)
return outputs
0