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[FIX] BET incorrect output paths #3214

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Merged
merged 2 commits into from
Jun 2, 2020
Merged

[FIX] BET incorrect output paths #3214

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5f85656
Added VSCode configuration directory and venv/ to .gitignore.
ZviBaratz May 16, 2020
b344a58
Fixed BET's returned output path bug, resolves #2916.
ZviBaratz May 16, 2020
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -29,3 +29,5 @@ __pycache__/
.ipynb_checkpoints/
.ruby-version
.pytest_cache
.vscode/
venv/
27 changes: 16 additions & 11 deletions nipype/interfaces/fsl/preprocess.py
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Expand Up @@ -173,45 +173,50 @@ def _gen_outfilename(self):
def _list_outputs(self):
outputs = self.output_spec().get()
outputs["out_file"] = self._gen_outfilename()

basename = os.path.basename(outputs['out_file'])
cwd = os.path.dirname(outputs['out_file'])
kwargs = {'basename': basename, 'cwd': cwd}

if (isdefined(self.inputs.mesh) and self.inputs.mesh) or (
isdefined(self.inputs.surfaces) and self.inputs.surfaces
):
outputs["meshfile"] = self._gen_fname(
outputs["out_file"], suffix="_mesh.vtk", change_ext=False
suffix="_mesh.vtk", change_ext=False, **kwargs
)
if (isdefined(self.inputs.mask) and self.inputs.mask) or (
isdefined(self.inputs.reduce_bias) and self.inputs.reduce_bias
):
outputs["mask_file"] = self._gen_fname(outputs["out_file"], suffix="_mask")
outputs["mask_file"] = self._gen_fname(suffix="_mask", **kwargs)
if isdefined(self.inputs.outline) and self.inputs.outline:
outputs["outline_file"] = self._gen_fname(
outputs["out_file"], suffix="_overlay"
suffix="_overlay", **kwargs
)
if isdefined(self.inputs.surfaces) and self.inputs.surfaces:
outputs["inskull_mask_file"] = self._gen_fname(
outputs["out_file"], suffix="_inskull_mask"
suffix="_inskull_mask", **kwargs
)
outputs["inskull_mesh_file"] = self._gen_fname(
outputs["out_file"], suffix="_inskull_mesh"
suffix="_inskull_mesh", **kwargs
)
outputs["outskull_mask_file"] = self._gen_fname(
outputs["out_file"], suffix="_outskull_mask"
suffix="_outskull_mask", **kwargs
)
outputs["outskull_mesh_file"] = self._gen_fname(
outputs["out_file"], suffix="_outskull_mesh"
suffix="_outskull_mesh", **kwargs
)
outputs["outskin_mask_file"] = self._gen_fname(
outputs["out_file"], suffix="_outskin_mask"
suffix="_outskin_mask", **kwargs
)
outputs["outskin_mesh_file"] = self._gen_fname(
outputs["out_file"], suffix="_outskin_mesh"
suffix="_outskin_mesh", **kwargs
)
outputs["skull_mask_file"] = self._gen_fname(
outputs["out_file"], suffix="_skull_mask"
suffix="_skull_mask", **kwargs
)
if isdefined(self.inputs.skull) and self.inputs.skull:
outputs["skull_file"] = self._gen_fname(
outputs["out_file"], suffix="_skull"
suffix="_skull", **kwargs
)
if isdefined(self.inputs.no_output) and self.inputs.no_output:
outputs["out_file"] = Undefined
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