From 15cba85bcbe4b2047cffd0b8bb420f4d94877e85 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 17 Nov 2018 20:31:24 -0500 Subject: [PATCH 1/3] enh: add extracted brain to antsCorticalThickness --- nipype/interfaces/ants/segmentation.py | 4 ++++ nipype/interfaces/ants/tests/test_auto_CorticalThickness.py | 1 + 2 files changed, 5 insertions(+) diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 04d212ec0f..743f0a3903 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -560,6 +560,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec): class CorticalThicknessOutputSpec(TraitedSpec): BrainExtractionMask = File(exists=True, desc='brain extraction mask') + ExtractedBrainN4 = File(exists=True, desc='extracted brain from N4 image') BrainSegmentation = File(exists=True, desc='brain segmentaion image') BrainSegmentationN4 = File(exists=True, desc='N4 corrected image') BrainSegmentationPosteriors = OutputMultiPath( @@ -645,6 +646,9 @@ def _list_outputs(self): outputs['BrainExtractionMask'] = os.path.join( os.getcwd(), self.inputs.out_prefix + 'BrainExtractionMask.' + self.inputs.image_suffix) + outputs['ExtractedBrainN4'] = os.path.join( + os.getcwd(), self.inputs.out_prefix + 'ExtractedBrain0N4.' + + self.inputs.image_suffix) outputs['BrainSegmentation'] = os.path.join( os.getcwd(), self.inputs.out_prefix + 'BrainSegmentation.' + self.inputs.image_suffix) diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index dd39568bc0..e2595a710f 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -75,6 +75,7 @@ def test_CorticalThickness_outputs(): BrainVolumes=dict(), CorticalThickness=dict(), CorticalThicknessNormedToTemplate=dict(), + ExtractedBrainN4=dict(), SubjectToTemplate0GenericAffine=dict(), SubjectToTemplate1Warp=dict(), SubjectToTemplateLogJacobian=dict(), From f70f32d8512986a8f0ba8d112c21853171ddd415 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 17 Nov 2018 20:31:53 -0500 Subject: [PATCH 2/3] fix: input name for spm RealignUnwarp --- nipype/interfaces/spm/preprocess.py | 4 +- .../spm/tests/test_auto_RealignUnwarp.py | 85 +++++++++++++++++++ 2 files changed, 87 insertions(+), 2 deletions(-) create mode 100644 nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py index 5330c67e34..d23887c890 100644 --- a/nipype/interfaces/spm/preprocess.py +++ b/nipype/interfaces/spm/preprocess.py @@ -524,12 +524,12 @@ class RealignUnwarpInputSpec(SPMCommandInputSpec): est_re_est_mov_par = traits.Bool( field='uweoptions.rem', desc='Re-estimate movement parameters at each unwarping iteration.') - est_num_of_interations = traits.ListInt( + est_num_of_iterations = traits.ListInt( [5], field='uweoptions.noi', minlen=1, maxlen=1, - usedfault=True, + usedefault=True, desc='Number of iterations.') est_taylor_expansion_point = traits.String( 'Average', diff --git a/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py new file mode 100644 index 0000000000..5c7c36f80b --- /dev/null +++ b/nipype/interfaces/spm/tests/test_auto_RealignUnwarp.py @@ -0,0 +1,85 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from __future__ import unicode_literals +from ..preprocess import RealignUnwarp + + +def test_RealignUnwarp_inputs(): + input_map = dict( + est_basis_func=dict(field='uweoptions.basfcn', ), + est_first_order_effects=dict(field='uweoptions.fot', ), + est_jacobian_deformations=dict(field='uweoptions.jm', ), + est_num_of_iterations=dict( + field='uweoptions.noi', + maxlen=1, + minlen=1, + usedefault=True, + ), + est_re_est_mov_par=dict(field='uweoptions.rem', ), + est_reg_factor=dict( + field='uweoptions.lambda', + maxlen=1, + minlen=1, + usedefault=True, + ), + est_reg_order=dict(field='uweoptions.regorder', ), + est_second_order_effects=dict(field='uweoptions.sot', ), + est_taylor_expansion_point=dict( + field='uweoptions.expround', + usedefault=True, + ), + est_unwarp_fwhm=dict(field='uweoptions.uwfwhm', ), + fwhm=dict(field='eoptions.fwhm', ), + in_files=dict( + copyfile=True, + field='data.scans', + mandatory=True, + ), + interp=dict(field='eoptions.einterp', ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), + out_prefix=dict( + field='uwroptions.prefix', + usedefault=True, + ), + paths=dict(), + phase_map=dict( + copyfile=False, + field='data.pmscan', + ), + quality=dict(field='eoptions.quality', ), + register_to_mean=dict(field='eoptions.rtm', ), + reslice_interp=dict(field='uwroptions.rinterp', ), + reslice_mask=dict(field='uwroptions.mask', ), + reslice_which=dict( + field='uwroptions.uwwhich', + maxlen=2, + minlen=2, + usedefault=True, + ), + reslice_wrap=dict(field='uwroptions.wrap', ), + separation=dict(field='eoptions.sep', ), + use_mcr=dict(), + use_v8struct=dict( + min_ver='8', + usedefault=True, + ), + weight_img=dict(field='eoptions.weight', ), + wrap=dict(field='eoptions.ewrap', ), + ) + inputs = RealignUnwarp.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value +def test_RealignUnwarp_outputs(): + output_map = dict( + mean_image=dict(), + modified_in_files=dict(), + realigned_unwarped_files=dict(), + realignment_parameters=dict(), + ) + outputs = RealignUnwarp.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value From aed7f161b399122c8b3ff112bea0aab260fa9377 Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Sat, 17 Nov 2018 20:32:15 -0500 Subject: [PATCH 3/3] fix: missing auto specs --- nipype/interfaces/dipy/tests/test_auto_DTI.py | 1 + nipype/interfaces/fsl/tests/test_auto_DTIFit.py | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index 68c9ae1437..f543856065 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -20,6 +20,7 @@ def test_DTI_inputs(): def test_DTI_outputs(): output_map = dict( ad_file=dict(), + color_fa_file=dict(), fa_file=dict(), md_file=dict(), out_file=dict(), diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index af6a0ea112..b1d3b4822d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -65,8 +65,8 @@ def test_DTIFit_outputs(): V1=dict(), V2=dict(), V3=dict(), - tensor=dict(), sse=dict(), + tensor=dict(), ) outputs = DTIFit.output_spec()