ENH: Miscellaneous FreeSurfer registration updates

nipype/interfaces/freesurfer/__init__.py

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

nipype/interfaces/freesurfer/preprocess.py

@@ -1159,6 +1159,8 @@ class BBRegisterInputSpec(FSTraitedSpec):
                                  desc="write the transformation matrix in LTA format")
     registered_file = traits.Either(traits.Bool, File, argstr='--o %s',
                                     desc='output warped sourcefile either True or filename')
+    init_cost_file = traits.Either(traits.Bool, File, argstr='--initcost %s',
+                                   desc='output initial registration cost file')
 
 
 class BBRegisterInputSpec6(BBRegisterInputSpec):
@@ -1172,10 +1174,11 @@ class BBRegisterInputSpec6(BBRegisterInputSpec):
 
 class BBRegisterOutputSpec(TraitedSpec):
     out_reg_file = File(exists=True, desc='Output registration file')
-    out_fsl_file = File(desc='Output FLIRT-style registration file')
-    out_lta_file = File(desc='Output LTA-style registration file')
+    out_fsl_file = File(exists=True, desc='Output FLIRT-style registration file')
+    out_lta_file = File(exists=True, desc='Output LTA-style registration file')
     min_cost_file = File(exists=True, desc='Output registration minimum cost file')
-    registered_file = File(desc='Registered and resampled source file')
+    init_cost_file = File(exists=True, desc='Output initial registration cost file')
+    registered_file = File(exists=True, desc='Registered and resampled source file')
 
 
 class BBRegister(FSCommand):
@@ -1242,17 +1245,19 @@ def _list_outputs(self):
             else:
                 outputs['out_fsl_file'] = op.abspath(_in.out_fsl_file)
 
+        if isdefined(_in.init_cost_file):
+            if isinstance(_in.out_fsl_file, bool):
+                outputs['init_cost_file'] = outputs['out_reg_file'] + '.initcost'
+            else:
+                outputs['init_cost_file'] = op.abspath(_in.init_cost_file)
+
         outputs['min_cost_file'] = outputs['out_reg_file'] + '.mincost'
         return outputs
 
     def _format_arg(self, name, spec, value):
-
-        if name in ['registered_file', 'out_fsl_file', 'out_lta_file']:
-            if isinstance(value, bool):
-                fname = self._list_outputs()[name]
-            else:
-                fname = value
-            return spec.argstr % fname
+        if name in ('registered_file', 'out_fsl_file', 'out_lta_file',
+                    'init_cost_file') and isinstance(value, bool):
+            value = self._list_outputs()[name]
         return super(BBRegister, self)._format_arg(name, spec, value)
 
     def _gen_filename(self, name):
@@ -1277,7 +1282,15 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
     fs_target = traits.Bool(argstr='--fstarg', xor=_targ_xor, mandatory=True,
                             requires=['reg_file'],
                             desc='use orig.mgz from subject in regfile as target')
-    _reg_xor = ('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject')
+    _reg_xor = ('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file',
+                'reg_header', 'mni_152_reg', 'subject')
+    reg_file = File(exists=True, xor=_reg_xor, argstr='--reg %s',
+                    mandatory=True,
+                    desc='tkRAS-to-tkRAS matrix   (tkregister2 format)')
+    lta_file = File(exists=True, xor=_reg_xor, argstr='--lta %s',
+                    mandatory=True, desc='Linear Transform Array file')
+    lta_inv_file = File(exists=True, xor=_reg_xor, argstr='--lta-inv %s',
+                        mandatory=True, desc='LTA, invert')
     reg_file = File(exists=True, xor=_reg_xor, argstr='--reg %s',
                     mandatory=True,
                     desc='tkRAS-to-tkRAS matrix   (tkregister2 format)')
@@ -1290,8 +1303,9 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
     reg_header = traits.Bool(xor=_reg_xor, argstr='--regheader',
                              mandatory=True,
                              desc='ScannerRAS-to-ScannerRAS matrix = identity')
-    subject = traits.Str(xor=_reg_xor, argstr='--s %s',
-                         mandatory=True,
+    mni_152_reg = traits.Bool(xor=_reg_xor, argstr='--regheader', mandatory=True,
+                              desc='target MNI152 space')
+    subject = traits.Str(xor=_reg_xor, argstr='--s %s', mandatory=True,
                          desc='set matrix = identity and use subject for any templates')
     inverse = traits.Bool(desc='sample from target to source',
                           argstr='--inv')

nipype/interfaces/freesurfer/registration.py

@@ -338,3 +338,160 @@ def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = os.path.abspath(self.inputs.out_file)
         return outputs
+
+
+class MRICoregInputSpec(FSTraitedSpec):
+    source_file = File(argstr='--mov %s', desc='source file to be registered',
+                       mandatory=True, copyfile=False)
+    reference_file = File(argstr='--ref %s', desc='reference (target) file',
+                          mandatory=True, copyfile=False, xor=['subject_id'])
+    out_lta_file = traits.Either(True, File, argstr='--lta %s', default=True,
+                                 usedefault=True,
+                                 desc='output registration file (LTA format)')
+    out_reg_file = traits.Either(True, File, argstr='--regdat %s',
+                                 desc='output registration file (REG format)')
+    out_params_file = traits.Either(True, File, argstr='--params %s',
+                                    desc='output parameters file')
+
+    subjects_dir = Directory(exists=True, argstr='--sd %s',
+                             desc='FreeSurfer SUBJECTS_DIR')
+    subject_id = traits.Str(
+        argstr='--s %s', position=1, mandatory=True, xor=['reference_file'],
+        requires=['subjects_dir'],
+        desc='freesurfer subject ID (implies ``reference_mask == '
+             'aparc+aseg.mgz`` unless otherwise specified)')
+    dof = traits.Enum(6, 9, 12, argstr='--dof %d',
+                      desc='number of transform degrees of freedom')
+    reference_mask = traits.Either(
+        False, traits.Str, argstr='--ref-mask %s', position=2,
+        desc='mask reference volume with given mask, or None if ``False``')
+    source_mask = traits.Str(argstr='--mov-mask',
+                             desc='mask source file with given mask')
+    num_threads = traits.Int(argstr='--threads %d',
+                             desc='number of OpenMP threads')
+    no_coord_dithering = traits.Bool(argstr='--no-coord-dither',
+                                     desc='turn off coordinate dithering')
+    no_intensity_dithering = traits.Bool(argstr='--no-intensity-dither',
+                                         desc='turn off intensity dithering')
+    sep = traits.List(argstr='--sep %s...', minlen=1, maxlen=2,
+                      desc='set spatial scales, in voxels (default [2, 4])')
+    initial_translation = traits.Tuple(
+        traits.Float, traits.Float, traits.Float, argstr='--trans %g %g %g',
+        desc='initial translation in mm (implies no_cras0)')
+    initial_rotation = traits.Tuple(
+        traits.Float, traits.Float, traits.Float, argstr='--rot %g %g %g',
+        desc='initial rotation in degrees')
+    initial_scale = traits.Tuple(
+        traits.Float, traits.Float, traits.Float, argstr='--scale %g %g %g',
+        desc='initial scale')
+    initial_shear = traits.Tuple(
+        traits.Float, traits.Float, traits.Float, argstr='--shear %g %g %g',
+        desc='initial shear (Hxy, Hxz, Hyz)')
+    no_cras0 = traits.Bool(argstr='--no-cras0',
+                           desc='do not set translation parameters to align '
+                                'centers of source and reference files')
+    max_iters = traits.Range(low=1, argstr='--nitersmax %d',
+                             desc='maximum iterations (default: 4)')
+    ftol = traits.Float(argstr='--ftol %e',
+                        desc='floating-point tolerance (default=1e-7)')
+    linmintol = traits.Float(argstr='--linmintol %e')
+    saturation_threshold = traits.Range(
+        low=0.0, high=100.0, argstr='--sat %g',
+        desc='saturation threshold (default=9.999)')
+    conform_reference = traits.Bool(argstr='--conf-ref',
+                                    desc='conform reference without rescaling')
+    no_brute_force = traits.Bool(argstr='--no-bf',
+                                 desc='do not brute force search')
+    brute_force_limit = traits.Float(
+        argstr='--bf-lim %g', xor=['no_brute_force'],
+        desc='constrain brute force search to +/- lim')
+    brute_force_samples = traits.Int(
+        argstr='--bf-nsamp %d', xor=['no_brute_force'],
+        desc='number of samples in brute force search')
+    no_smooth = traits.Bool(
+        argstr='--no-smooth',
+        desc='do not apply smoothing to either reference or source file')
+    ref_fwhm = traits.Float(argstr='--ref-fwhm',
+                            desc='apply smoothing to reference file')
+    source_oob = traits.Bool(
+        argstr='--mov-oob',
+        desc='count source voxels that are out-of-bounds as 0')
+    # Skipping mat2par
+
+
+class MRICoregOutputSpec(TraitedSpec):
+    out_reg_file = File(exists=True, desc='output registration file')
+    out_lta_file = File(exists=True, desc='output LTA-style registration file')
+    out_params_file = File(exists=True, desc='output parameters file')
+
+
+class MRICoreg(FSCommand):
+    """ This program registers one volume to another
+
+    mri_coreg is a C reimplementation of spm_coreg in FreeSurfer
+
+    Examples
+    ========
+    >>> from nipype.interfaces.freesurfer import MRICoreg
+    >>> coreg = MRICoreg()
+    >>> coreg.inputs.source_file = 'moving1.nii'
+    >>> coreg.inputs.reference_file = 'fixed1.nii'
+    >>> coreg.inputs.subjects_dir = '.'
+    >>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
+    'mri_coreg --lta .../registration.lta --ref fixed1.nii --mov moving1.nii --sd .'
+
+    If passing a subject ID, the reference mask may be disabled:
+
+    >>> coreg = MRICoreg()
+    >>> coreg.inputs.source_file = 'moving1.nii'
+    >>> coreg.inputs.subjects_dir = '.'
+    >>> coreg.inputs.subject_id = 'fsaverage'
+    >>> coreg.inputs.reference_mask = False
+    >>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
+    'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --mov moving1.nii --sd .'
+
+    Spatial scales may be specified as a list of one or two separations:
+
+    >>> coreg.inputs.sep = [4]
+    >>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
+    'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --mov moving1.nii --sd .'
+
+    >>> coreg.inputs.sep = [4, 5]
+    >>> coreg.cmdline # doctest: +ALLOW_UNICODE +ELLIPSIS
+    'mri_coreg --s fsaverage --no-ref-mask --lta .../registration.lta --sep 4 --sep 5 --mov moving1.nii --sd .'
+    """
+
+    _cmd = 'mri_coreg'
+    input_spec = MRICoregInputSpec
+    output_spec = MRICoregOutputSpec
+
+    def _format_arg(self, opt, spec, val):
+        if opt in ('out_reg_file', 'out_lta_file',
+                   'out_params_file') and val is True:
+            val = self._list_outputs()[opt]
+        elif opt == 'reference_mask' and val is False:
+            return '--no-ref-mask'
+        return super(MRICoreg, self)._format_arg(opt, spec, val)
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+
+        out_lta_file = self.inputs.out_lta_file
+        if isdefined(out_lta_file):
+            if out_lta_file is True:
+                out_lta_file = 'registration.lta'
+            outputs['out_lta_file'] = os.path.abspath(out_lta_file)
+
+        out_reg_file = self.inputs.out_reg_file
+        if isdefined(out_reg_file):
+            if out_reg_file is True:
+                out_reg_file = 'registration.dat'
+            outputs['out_reg_file'] = os.path.abspath(out_reg_file)
+
+        out_params_file = self.inputs.out_params_file
+        if isdefined(out_params_file):
+            if out_params_file is True:
+                out_params_file = 'registration.par'
+            outputs['out_params_file'] = os.path.abspath(out_params_file)
+
+        return outputs

nipype/interfaces/freesurfer/tests/test_BBRegister.py

@@ -12,6 +12,7 @@ def test_BBRegister_inputs():
         fsldof=dict(argstr='--fsl-dof %d',),
         ignore_exception=dict(nohash=True, usedefault=True,),
         init=dict(argstr='--init-%s', mandatory=True, xor=['init_reg_file'],),
+        init_cost_file=dict(argstr='--initcost %s',),
         init_reg_file=dict(argstr='--init-reg %s', mandatory=True, xor=['init'],),
         intermediate_file=dict(argstr='--int %s',),
         out_fsl_file=dict(argstr='--fslmat %s',),
@@ -36,6 +37,7 @@ def test_BBRegister_inputs():
         ignore_exception=dict(nohash=True, usedefault=True,),
         init=dict(argstr='--init-%s', xor=['init_reg_file'],),
         init_reg_file=dict(argstr='--init-reg %s', xor=['init'],),
+        init_cost_file=dict(argstr='--initcost %s',),
         intermediate_file=dict(argstr='--int %s',),
         out_fsl_file=dict(argstr='--fslmat %s',),
         out_lta_file=dict(argstr='--lta %s', min_ver='5.2.0',),
@@ -62,7 +64,8 @@ def test_BBRegister_inputs():
 
 
 def test_BBRegister_outputs():
-    output_map = dict(min_cost_file=dict(),
+    output_map = dict(init_cost_file=dict(),
+                      min_cost_file=dict(),
                       out_fsl_file=dict(),
                       out_lta_file=dict(),
                       out_reg_file=dict(),

nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py

@@ -16,7 +16,7 @@ def test_ApplyVolTransform_inputs():
     ),
     fsl_reg_file=dict(argstr='--fsl %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
@@ -28,28 +28,40 @@ def test_ApplyVolTransform_inputs():
     invert_morph=dict(argstr='--inv-morph',
     requires=['m3z_file'],
     ),
+    lta_file=dict(argstr='--lta %s',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
+    lta_inv_file=dict(argstr='--lta-inv %s',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
     m3z_file=dict(argstr='--m3z %s',
     ),
+    mni_152_reg=dict(argstr='--regheader',
+    mandatory=True,
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
+    ),
     no_ded_m3z_path=dict(argstr='--noDefM3zPath',
     requires=['m3z_file'],
     ),
     no_resample=dict(argstr='--no-resample',
     ),
     reg_file=dict(argstr='--reg %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     reg_header=dict(argstr='--regheader',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     source_file=dict(argstr='--mov %s',
     copyfile=False,
     mandatory=True,
     ),
     subject=dict(argstr='--s %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     subjects_dir=dict(),
     tal=dict(argstr='--tal',
@@ -69,7 +81,7 @@ def test_ApplyVolTransform_inputs():
     ),
     xfm_reg_file=dict(argstr='--xfm %s',
     mandatory=True,
-    xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'),
+    xor=('reg_file', 'lta_file', 'lta_inv_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'mni_152_reg', 'subject'),
     ),
     )
     inputs = ApplyVolTransform.input_spec()