From 881636526133d900f525ecaff79790fb7b7bbcf7 Mon Sep 17 00:00:00 2001 From: Steven Tilley Date: Tue, 12 Nov 2019 17:39:56 -0500 Subject: [PATCH 1/3] add skull_file output --- nipype/interfaces/fsl/preprocess.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index ce96763d43..3d247506f4 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -111,6 +111,7 @@ class BETOutputSpec(TraitedSpec): 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): @@ -181,6 +182,9 @@ def _list_outputs(self): outputs['out_file'], suffix='_outskin_mesh') 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 From a7d0f63f56124d3c6aaae3b5312798916af7bb74 Mon Sep 17 00:00:00 2001 From: Steven Tilley Date: Wed, 13 Nov 2019 09:56:39 -0500 Subject: [PATCH 2/3] run make specs --- nipype/interfaces/fsl/tests/test_auto_BET.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index ea155c249b..b4f1689b0c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -94,6 +94,7 @@ 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() From 7f85f43a34de8bff8e634232c939b17cee8e8fc5 Mon Sep 17 00:00:00 2001 From: Steven Tilley Date: Fri, 15 Nov 2019 14:34:03 -0500 Subject: [PATCH 3/3] run black --- nipype/interfaces/fsl/preprocess.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index 277d81c2ce..bf38ff3d1f 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -210,8 +210,8 @@ def _list_outputs(self): 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' + 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