From 78c356827184f2f4003c38d03dfc0a38f0a5115b Mon Sep 17 00:00:00 2001 From: salma1601 Date: Sun, 13 Aug 2017 23:56:03 +0200 Subject: [PATCH 1/2] add more inputs --- nipype/interfaces/afni/preprocess.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 2c6274ed30..1cc4fd6c5e 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -144,7 +144,7 @@ class AllineateInputSpec(AFNICommandInputSpec): desc='Use a two pass alignment strategy for all volumes, searching ' 'for a large rotation+shift and then refining the alignment.') two_blur = traits.Float( - argstr='-twoblur', + argstr='-twoblur %f', desc='Set the blurring radius for the first pass in mm.') two_first = traits.Bool( argstr='-twofirst', @@ -222,6 +222,18 @@ class AllineateInputSpec(AFNICommandInputSpec): 'EPI slices, and the base as comprising anatomically ' '\'true\' images. Only phase-encoding direction image ' 'shearing and scaling will be allowed with this option.') + maxrot = traits.Float( + argstr='-maxrot %f', + desc='Maximum allowed rotation in degrees.') + maxshf = traits.Float( + argstr='-maxshf %f', + desc='Maximum allowed shift in mm.') + maxscl = traits.Float( + argstr='-maxscl %f', + desc='Maximum allowed scaling factor.') + maxshr = traits.Float( + argstr='-maxshr %f', + desc='Maximum allowed shearing factor.') master = File( exists=True, argstr='-master %s', From 25e9b577652221422ead7a625d8225d8c49f391a Mon Sep 17 00:00:00 2001 From: salma1601 Date: Tue, 15 Aug 2017 14:11:42 +0200 Subject: [PATCH 2/2] update autotest --- nipype/interfaces/afni/tests/test_auto_Allineate.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 0bf37ea8cd..bfa2317311 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -46,6 +46,14 @@ def test_Allineate_inputs(): ), master=dict(argstr='-master %s', ), + maxrot=dict(argstr='-maxrot %f', + ), + maxscl=dict(argstr='-maxscl %f', + ), + maxshf=dict(argstr='-maxshf %f', + ), + maxshr=dict(argstr='-maxshr %f', + ), newgrid=dict(argstr='-newgrid %f', ), nmatch=dict(argstr='-nmatch %d', @@ -88,7 +96,7 @@ def test_Allineate_inputs(): ), two_best=dict(argstr='-twobest %d', ), - two_blur=dict(argstr='-twoblur', + two_blur=dict(argstr='-twoblur %f', ), two_first=dict(argstr='-twofirst', ),