From d159fe9e8927800a7ec18048fc33b843209f517d Mon Sep 17 00:00:00 2001 From: Salma BOUGACHA Date: Wed, 22 Nov 2017 10:52:10 +0100 Subject: [PATCH 1/3] add rbt option --- nipype/interfaces/afni/utils.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 242b5077ee..f836cadb8d 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -2329,6 +2329,13 @@ class UnifizeInputSpec(AFNICommandInputSpec): argstr='-EPI', requires=['no_duplo', 't2'], xor=['gm']) + rbt = traits.Tuple( + traits.Float(), traits.Float(), traits.Float(), + desc='Specify the 3 parameters for the algorithm:\n' + 'R = radius; same as given by option \'-Urad\', [default=18.3]\n' + 'b = bottom percentile of normalizing data range, [default=70.0]\n' + 'r = top percentile of normalizing data range, [default=80.0]\n', + argstr='-rbt %f %f %f') class UnifizeOutputSpec(TraitedSpec): From 4c9ccdf060d2ce586945e9e0b6533a6b5c59e36a Mon Sep 17 00:00:00 2001 From: salma1601 Date: Wed, 22 Nov 2017 11:26:09 +0100 Subject: [PATCH 2/3] update test --- nipype/interfaces/afni/tests/test_auto_Unifize.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/nipype/interfaces/afni/tests/test_auto_Unifize.py b/nipype/interfaces/afni/tests/test_auto_Unifize.py index 6105a9d5c2..e5be64e70d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Unifize.py +++ b/nipype/interfaces/afni/tests/test_auto_Unifize.py @@ -32,6 +32,8 @@ def test_Unifize_inputs(): name_source='in_file', ), outputtype=dict(), + rbt=dict(argstr='-rbt %f %f %f', + ), scale_file=dict(argstr='-ssave %s', ), t2=dict(argstr='-T2', From d1b65be43a7b2bf44344b0863e6a85b7fb07e2e3 Mon Sep 17 00:00:00 2001 From: salma1601 Date: Wed, 22 Nov 2017 11:28:53 +0100 Subject: [PATCH 3/3] add note option for experts --- nipype/interfaces/afni/utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index f836cadb8d..3e03adda92 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -2331,7 +2331,8 @@ class UnifizeInputSpec(AFNICommandInputSpec): xor=['gm']) rbt = traits.Tuple( traits.Float(), traits.Float(), traits.Float(), - desc='Specify the 3 parameters for the algorithm:\n' + desc='Option for AFNI experts only.' + 'Specify the 3 parameters for the algorithm:\n' 'R = radius; same as given by option \'-Urad\', [default=18.3]\n' 'b = bottom percentile of normalizing data range, [default=70.0]\n' 'r = top percentile of normalizing data range, [default=80.0]\n',