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Add skull_file output to fsl.BET interface #3095

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Merged
merged 4 commits into from
Nov 16, 2019
+6 −0
Merged

Add skull_file output to fsl.BET interface #3095

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8816365
add skull_file output
stilley2 Nov 12, 2019
a7d0f63
run make specs
stilley2 Nov 13, 2019
0b15b3e
Merge remote-tracking branch 'origin/master' into FIX/betskull
stilley2 Nov 15, 2019
7f85f43
run black
stilley2 Nov 15, 2019
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5 changes: 5 additions & 0 deletions nipype/interfaces/fsl/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,7 @@ class BETOutputSpec(TraitedSpec):
outskin_mask_file = File(desc="path/name of outskin mask (if generated)")
outskin_mesh_file = File(desc="path/name of outskin mesh outline (if generated)")
skull_mask_file = File(desc="path/name of skull mask (if generated)")
skull_file = File(desc="path/name of skull file (if generated)")


class BET(FSLCommand):
Expand Down Expand Up @@ -208,6 +209,10 @@ def _list_outputs(self):
outputs["skull_mask_file"] = self._gen_fname(
outputs["out_file"], suffix="_skull_mask"
)
if isdefined(self.inputs.skull) and self.inputs.skull:
outputs["skull_file"] = self._gen_fname(
outputs["out_file"], suffix="_skull"
)
if isdefined(self.inputs.no_output) and self.inputs.no_output:
outputs["out_file"] = Undefined
return outputs
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1 change: 1 addition & 0 deletions nipype/interfaces/fsl/tests/test_auto_BET.py
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Expand Up @@ -126,6 +126,7 @@ def test_BET_outputs():
outskin_mesh_file=dict(extensions=None,),
outskull_mask_file=dict(extensions=None,),
outskull_mesh_file=dict(extensions=None,),
skull_file=dict(extensions=None,),
skull_mask_file=dict(extensions=None,),
)
outputs = BET.output_spec()
Expand Down