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chrisgorgochrisgorgo
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Merge pull request #1231 from MartinPerez/ants_brain_extract
Ants brain extraction interface
2 parents 8d26eec + 6c24260 commit 665ee55

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‎nipype/interfaces/ants/__init__.py

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@@ -11,7 +11,7 @@
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# Segmentation Programs
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from .segmentation import Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion
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from .segmentation import Atropos, LaplacianThickness, N4BiasFieldCorrection, JointFusion, antsCorticalThickness, antsBrainExtraction
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# Visualization Programs
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from .visualization import ConvertScalarImageToRGB, CreateTiledMosaic

‎nipype/interfaces/ants/segmentation.py

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@@ -465,7 +465,7 @@ class antsCorticalThicknessInputSpec(ANTSCommandInputSpec):
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'Requires single thread computation for complete reproducibility.'))
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class antsCorticalThicknessoutputSpec(TraitedSpec):
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class antsCorticalThicknessOutputSpec(TraitedSpec):
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BrainExtractionMask = File(exists=True, desc='brain extraction mask')
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BrainSegmentation = File(exists=True, desc='brain segmentaion image')
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BrainSegmentationN4 = File(exists=True, desc='N4 corrected image')
@@ -503,7 +503,7 @@ class antsCorticalThickness(ANTSCommand):
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"""
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input_spec = antsCorticalThicknessInputSpec
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output_spec = antsCorticalThicknessoutputSpec
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output_spec = antsCorticalThicknessOutputSpec
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_cmd = 'antsCorticalThickness.sh'
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def _format_arg(self, opt, spec, val):
@@ -594,6 +594,86 @@ def _list_outputs(self):
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return outputs
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class antsBrainExtractionInputSpec(ANTSCommandInputSpec):
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dimension = traits.Enum(3, 2, argstr='-d %d', usedefault=True,
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desc='image dimension (2 or 3)')
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anatomical_image = File(exists=True, argstr='-a %s',
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desc=('Structural image, typically T1. If more than one'
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'anatomical image is specified, subsequently specified'
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'images are used during the segmentation process. However,'
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'only the first image is used in the registration of priors.'
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'Our suggestion would be to specify the T1 as the first image.'
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'Anatomical template created using e.g. LPBA40 data set with'
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'buildtemplateparallel.sh in ANTs.'),
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mandatory=True)
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brain_template = File(exists=True, argstr='-e %s',
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desc=('Anatomical template created using e.g. LPBA40 data set with'
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'buildtemplateparallel.sh in ANTs.'),
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mandatory=True)
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brain_probability_mask = File(exists=True, argstr='-m %s',
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desc=('Brain probability mask created using e.g. LPBA40 data set which'
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'have brain masks defined, and warped to anatomical template and'
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'averaged resulting in a probability image.'),
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copyfile=False, mandatory=True)
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out_prefix = traits.Str('highres001_', argstr='-o %s', usedefault=True,
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desc=('Prefix that is prepended to all output'
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' files (default = highress001_)'))
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extraction_registration_mask = File(exists=True, argstr='-f %s',
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desc=('Mask (defined in the template space) used during'
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' registration for brain extraction.'
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'To limit the metric computation to a specific region.'))
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image_suffix = traits.Str('nii.gz', desc=('any of standard ITK formats,'
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' nii.gz is default'),
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argstr='-s %s', usedefault=True)
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use_random_seeding = traits.Enum(0, 1, argstr='-u %d',
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desc=('Use random number generated from system clock in Atropos'
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'(default = 1)'))
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keep_temporary_files = traits.Int(argstr='-k %d',
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desc='Keep brain extraction/segmentation warps, etc (default = 0).')
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use_floatingpoint_precision = traits.Enum(0, 1, argstr='-q %d',
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desc=('Use floating point precision '
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'in registrations (default = 0)'))
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debug = traits.Bool(argstr='-z 1',
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desc=('If > 0, runs a faster version of the script.'
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'Only for testing. Implies -u 0.'
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'Requires single thread computation for complete reproducibility.'))
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class antsBrainExtractionOutputSpec(TraitedSpec):
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BrainExtractionMask = File(exists=True, desc='brain extraction mask')
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BrainExtractionBrain = File(exists=True, desc='brain extraction image')
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class antsBrainExtraction(ANTSCommand):
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"""
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Examples
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--------
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>>> from nipype.interfaces.ants.segmentation import antsBrainExtraction
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>>> brainextraction = antsBrainExtraction()
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>>> brainextraction.inputs.dimension = 3
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>>> brainextraction.inputs.anatomical_image ='T1.nii.gz'
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>>> brainextraction.inputs.brain_template = 'study_template.nii.gz'
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>>> brainextraction.inputs.brain_probability_mask ='ProbabilityMaskOfStudyTemplate.nii.gz'
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>>> brainextraction.cmdline
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'antsBrainExtraction.sh -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -d 3 -s nii.gz -o highres001_'
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"""
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input_spec = antsBrainExtractionInputSpec
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output_spec = antsBrainExtractionOutputSpec
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_cmd = 'antsBrainExtraction.sh'
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def _list_outputs(self):
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outputs = self._outputs().get()
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outputs['BrainExtractionMask'] = os.path.join(os.getcwd(),
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self.inputs.out_prefix +
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'BrainExtractionMask.' +
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self.inputs.image_suffix)
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outputs['BrainExtractionBrain'] = os.path.join(os.getcwd(),
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self.inputs.out_prefix +
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'BrainExtractionBrain.' +
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self.inputs.image_suffix)
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return outputs
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class JointFusionInputSpec(ANTSCommandInputSpec):
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dimension = traits.Enum(3, 2, 4, argstr='%d', position=0, usedefault=True,
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mandatory=True,

‎nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from nipype.testing import assert_equal
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from nipype.interfaces.ants.segmentation import antsBrainExtraction
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def test_antsBrainExtraction_inputs():
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input_map = dict(anatomical_image=dict(argstr='-a %s',
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mandatory=True,
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),
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args=dict(argstr='%s',
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),
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brain_probability_mask=dict(argstr='-m %s',
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copyfile=False,
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mandatory=True,
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),
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brain_template=dict(argstr='-e %s',
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mandatory=True,
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),
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debug=dict(argstr='-z 1',
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),
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dimension=dict(argstr='-d %d',
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usedefault=True,
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),
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environ=dict(nohash=True,
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usedefault=True,
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),
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extraction_registration_mask=dict(argstr='-f %s',
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),
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ignore_exception=dict(nohash=True,
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usedefault=True,
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),
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image_suffix=dict(argstr='-s %s',
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usedefault=True,
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),
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keep_temporary_files=dict(argstr='-k %d',
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),
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out_prefix=dict(argstr='-o %s',
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usedefault=True,
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),
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terminal_output=dict(nohash=True,
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),
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use_floatingpoint_precision=dict(argstr='-q %d',
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),
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use_random_seeding=dict(argstr='-u %d',
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),
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)
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inputs = antsBrainExtraction.input_spec()
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for key, metadata in input_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(inputs.traits()[key], metakey), value
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def test_antsBrainExtraction_outputs():
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output_map = dict(BrainExtractionMask=dict(),
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BrainExtractionBrain=dict(),
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)
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outputs = antsBrainExtraction.output_spec()
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for key, metadata in output_map.items():
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for metakey, value in metadata.items():
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yield assert_equal, getattr(outputs.traits()[key], metakey), value

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