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ENH: Add mri_coreg interface
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‎nipype/interfaces/freesurfer/__init__.py

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@@ -24,4 +24,4 @@
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RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand, MRIsCombine)
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from .longitudinal import (RobustTemplate, FuseSegmentations)
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from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
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Paint)
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Paint, MRICoreg)

‎nipype/interfaces/freesurfer/registration.py

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@@ -338,3 +338,145 @@ def _list_outputs(self):
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outputs = self.output_spec().get()
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outputs['out_file'] = os.path.abspath(self.inputs.out_file)
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return outputs
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class MRICoregInputSpec(FSTraitedSpec):
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source_file = File(argstr='--mov %s', desc='source file to be registered',
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mandatory=True, copyfile=False)
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reference_file = File(argstr='--ref %s', desc='reference (target) file',
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mandatory=True, copyfile=False)
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out_lta_file = traits.Either(True, File, argstr='--lta %s', default=True,
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usedefault=True,
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desc='output registration file (LTA format)')
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out_reg_file = traits.Either(True, File, argstr='--regdat %s',
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desc='output registration file (REG format)')
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out_params_file = traits.Either(True, File, argstr='--params %s',
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desc='output parameters file')
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subjects_dir = Directory(exists=True, argstr='--sd %s',
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desc='FreeSurfer SUBJECTS_DIR')
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subject_id = traits.Str(
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argstr='--s %s', position=1,
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desc='freesurfer subject ID (implies ``reference_mask == '
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'aparc+aseg.mgz`` unless otherwise specified)')
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dof = traits.Enum(6, 9, 12, argstr='--dof %d',
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desc='number of transform degrees of freedom')
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reference_mask = traits.Either(
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False, traits.Str, argstr='--ref-mask %s', position=2,
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desc='mask reference volume with given mask, or None if ``False``')
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source_mask = traits.Str(argstr='--mov-mask',
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desc='mask source file with given mask')
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num_threads = traits.Int(argstr='--threads %d',
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desc='number of OpenMP threads')
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no_coord_dithering = traits.Bool(argstr='--no-coord-dither',
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desc='turn off coordinate dithering')
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no_intensity_dithering = traits.Bool(argstr='--no-intensity-dither',
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desc='turn off intensity dithering')
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# Skipping: --sep
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initial_translation = traits.Tuple(
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traits.Float, traits.Float, traits.Float, argstr='--trans %g %g %g',
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desc='initial translation in mm (implies no_cras0)')
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initial_rotation = traits.Tuple(
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traits.Float, traits.Float, traits.Float, argstr='--rot %g %g %g',
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desc='initial rotation in degrees')
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initial_scale = traits.Tuple(
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traits.Float, traits.Float, traits.Float, argstr='--scale %g %g %g',
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desc='initial scale')
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initial_shear = traits.Tuple(
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traits.Float, traits.Float, traits.Float, argstr='--shear %g %g %g',
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desc='initial shear (Hxy, Hxz, Hyz)')
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no_cras0 = traits.Bool(argstr='--no-cras0',
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desc='do not set translation parameters to align '
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'centers of source and reference files')
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max_iters = traits.Range(low=1, argstr='--nitersmax %d',
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desc='maximum iterations (default: 4)')
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ftol = traits.Float(argstr='--ftol %e',
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desc='floating-point tolerance (default=1e-7)')
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linmintol = traits.Float(argstr='--linmintol %e')
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saturation_threshold = traits.Range(
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low=0.0, high=100.0, argstr='--sat %g',
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desc='saturation threshold (default=9.999)')
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conform_reference = traits.Bool(argstr='--conf-ref',
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desc='conform reference without rescaling')
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no_brute_force = traits.Bool(argstr='--no-bf',
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desc='do not brute force search')
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brute_force_limit = traits.Float(
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argstr='--bf-lim %g', xor=['no_brute_force'],
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desc='constrain brute force search to +/- lim')
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brute_force_samples = traits.Int(
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argstr='--bf-nsamp %d', xor=['no_brute_force'],
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desc='number of samples in brute force search')
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no_smooth = traits.Bool(
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argstr='--no-smooth',
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desc='do not apply smoothing to either reference or source file')
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ref_fwhm = traits.Float(argstr='--ref-fwhm',
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desc='apply smoothing to reference file')
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source_oob = traits.Bool(
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argstr='--mov-oob',
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desc='count source voxels that are out-of-bounds as 0')
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# Skipping mat2par
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class MRICoregOutputSpec(TraitedSpec):
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out_reg_file = File(exists=True, desc='output registration file')
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out_lta_file = File(exists=True, desc='output LTA-style registration file')
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out_params_file = File(exists=True, desc='output parameters file')
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class MRICoreg(FSCommand):
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""" This program registers one volume to another
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mri_coreg is a C reimplementation of spm_coreg in FreeSurfer
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Examples
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========
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>>> from nipype.interfaces.freesurfer import MRICoreg
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>>> coreg = MRICoreg()
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>>> coreg.inputs.source_file = 'moving1.nii'
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>>> coreg.inputs.reference_file = 'fixed1.nii'
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>>> coreg.inputs.subjects_dir = '.'
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>>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
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'mri_coreg --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .'
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If passing a subject ID, the reference mask may be disabled:
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>>> coreg.inputs.subject_id = 'fsaverage'
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>>> coreg.inputs.reference_mask = False
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>>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
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'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .'
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"""
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_cmd = 'mri_coreg'
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input_spec = MRICoregInputSpec
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output_spec = MRICoregOutputSpec
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def _format_arg(self, opt, spec, val):
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if opt in ('out_reg_file', 'out_lta_file',
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'out_params_file') and val is True:
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val = self._list_outputs()[opt]
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elif opt == 'reference_mask' and val is False:
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return '--no-ref-mask'
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return super(MRICoreg, self)._format_arg(opt, spec, val)
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def _list_outputs(self):
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outputs = self.output_spec().get()
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out_lta_file = self.inputs.out_lta_file
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if isdefined(out_lta_file):
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if out_lta_file is True:
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out_lta_file = 'registration.lta'
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outputs['out_lta_file'] = os.path.abspath(out_lta_file)
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out_reg_file = self.inputs.out_reg_file
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if isdefined(out_reg_file):
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if out_reg_file is True:
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out_reg_file = 'registration.dat'
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outputs['out_reg_file'] = os.path.abspath(out_reg_file)
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out_params_file = self.inputs.out_params_file
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if isdefined(out_params_file):
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if out_params_file is True:
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out_params_file = 'registration.par'
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outputs['out_params_file'] = os.path.abspath(out_params_file)
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return outputs

‎nipype/interfaces/freesurfer/tests/test_auto_MRICoreg.py

Lines changed: 101 additions & 0 deletions
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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from __future__ import unicode_literals
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from ..registration import MRICoreg
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def test_MRICoreg_inputs():
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input_map = dict(args=dict(argstr='%s',
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),
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brute_force_limit=dict(argstr='--bf-lim %g',
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xor=['no_brute_force'],
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),
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brute_force_samples=dict(argstr='--bf-nsamp %d',
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xor=['no_brute_force'],
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),
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conform_reference=dict(argstr='--conf-ref',
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),
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dof=dict(argstr='--dof %d',
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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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ftol=dict(argstr='--ftol %e',
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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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initial_rotation=dict(argstr='--rot %g %g %g',
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),
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initial_scale=dict(argstr='--scale %g %g %g',
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),
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initial_shear=dict(argstr='--shear %g %g %g',
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),
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initial_translation=dict(argstr='--trans %g %g %g',
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),
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linmintol=dict(argstr='--linmintol %e',
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),
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max_iters=dict(argstr='--nitersmax %d',
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),
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no_brute_force=dict(argstr='--no-bf',
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),
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no_coord_dithering=dict(argstr='--no-coord-dither',
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),
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no_cras0=dict(argstr='--no-cras0',
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),
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no_intensity_dithering=dict(argstr='--no-intensity-dither',
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),
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no_smooth=dict(argstr='--no-smooth',
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),
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num_threads=dict(argstr='--threads %d',
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),
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out_lta_file=dict(argstr='--lta %s',
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usedefault=True,
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),
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out_params_file=dict(argstr='--params %s',
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),
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out_reg_file=dict(argstr='--regdat %s',
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),
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ref_fwhm=dict(argstr='--ref-fwhm',
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),
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reference_file=dict(argstr='--ref %s',
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copyfile=False,
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mandatory=True,
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),
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reference_mask=dict(argstr='--ref-mask %s',
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position=2,
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),
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saturation_threshold=dict(argstr='--sat %g',
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),
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source_file=dict(argstr='--mov %s',
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copyfile=False,
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mandatory=True,
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),
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source_mask=dict(argstr='--mov-mask',
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),
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source_oob=dict(argstr='--mov-oob',
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),
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subject_id=dict(argstr='--s %s',
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position=1,
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),
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subjects_dir=dict(argstr='--sd %s',
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),
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terminal_output=dict(nohash=True,
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),
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)
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inputs = MRICoreg.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_MRICoreg_outputs():
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output_map = dict(out_lta_file=dict(),
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out_params_file=dict(),
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out_reg_file=dict(),
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)
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outputs = MRICoreg.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

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