Merge branch 'enh/mri_surf2vol'

Author: chrisgorgo

nipype/interfaces/afni/preprocess.py

@@ -330,7 +330,6 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
     mask_only_targets = traits.Bool(desc="use mask only on targets voxels",
                                     argstr="-mask_only_targets",
                                     xor=['mask_source'])
-
     mask_source = File(exists=True,
                         desc="mask for source voxels",
                         argstr="-mask_source %s",

nipype/interfaces/freesurfer/__init__.py

@@ -4,12 +4,12 @@
 
 from .base import Info, FSCommand
 from .preprocess import (ParseDICOMDir, UnpackSDICOMDir, MRIConvert, Resample,
-                         ReconAll, BBRegister, ApplyVolTransform, Smooth,
+                         ReconAll, BBRegister, ApplyVolTransform,Smooth,
                          DICOMConvert, RobustRegister, FitMSParams,
                          SynthesizeFLASH)
 from .model import (MRISPreproc, GLMFit, OneSampleTTest, Binarize, Concatenate,
                     SegStats, Label2Vol, MS_LDA)
-from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform,
+from .utils import (SampleToSurface, SurfaceSmooth, SurfaceTransform, Surface2VolTransform, 
                     SurfaceSnapshots,ApplyMask, MRIsConvert, MRITessellate,
                     MRIMarchingCubes, SmoothTessellation, MakeAverageSubject,
                     ExtractMainComponent)

nipype/interfaces/freesurfer/preprocess.py

@@ -970,7 +970,6 @@ class ApplyVolTransformInputSpec(FSTraitedSpec):
                                      'non-linear morph to resample the input '
                                      'volume. To be used by --m3z.'))
 
-
 class ApplyVolTransformOutputSpec(TraitedSpec):
     transformed_file = File(exists=True, desc='Path to output file if used normally')
 
@@ -1021,7 +1020,6 @@ def _gen_filename(self, name):
             return self._get_outfile()
         return None
 
-
 class SmoothInputSpec(FSTraitedSpec):
     in_file = File(exists=True, desc='source volume',
                      argstr='--i %s', mandatory=True)

nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py

@@ -0,0 +1,66 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from nipype.testing import assert_equal
+from nipype.interfaces.freesurfer.utils import Surface2VolTransform
+def test_Surface2VolTransform_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    transformed_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol.nii',
+    argstr='--outvol %s',
+    ),
+    hemi=dict(mandatory=True,
+    argstr='--hemi %s',
+    ),
+    template_file=dict(argstr='--template %s',
+    ),
+    subject_id=dict(xor=['reg_file'],
+    argstr='--identity %s',
+    ),
+    args=dict(argstr='%s',
+    ),
+    surf_name=dict(argstr='--surf %s',
+    exists=True,
+    ),
+    vertexvol_file=dict(name_source=['source_file'],
+    hash_files=False,
+    name_template='%s_asVol_vertex.nii',
+    argstr='--vtxvol %s',
+    ),
+    reg_file=dict(mandatory=True,
+    argstr='--volreg %s',
+    xor=['subject_id'],
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    subjects_dir=dict(argstr='--sd %s',
+    ),
+    source_file=dict(copyfile=False,
+    mandatory=True,
+    argstr='--surfval %s',
+    ),
+    projfrac=dict(argstr='--projfrac %s',
+    exists=True,
+    ),
+    mkmask=dict(argstr='--mkmask',
+    ),
+    terminal_output=dict(mandatory=True,
+    nohash=True,
+    ),
+    )
+    inputs = Surface2VolTransform.input_spec()
+
+    for key, metadata in input_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+def test_Surface2VolTransform_outputs():
+    output_map = dict(transformed_file=dict(),
+    vertexvol_file=dict(),
+    )
+    outputs = Surface2VolTransform.output_spec()
+
+    for key, metadata in output_map.items():
+        for metakey, value in metadata.items():
+            yield assert_equal, getattr(outputs.traits()[key], metakey), value

nipype/interfaces/freesurfer/utils.py

@@ -382,6 +382,55 @@ def _gen_filename(self, name):
             return self._list_outputs()[name]
         return None
 
+class Surface2VolTransformInputSpec(FSTraitedSpec):
+    source_file = File(exists=True, argstr='--surfval %s',
+                      copyfile=False, mandatory=True,
+                      desc='This is the source of the surface values')
+    hemi = traits.Str(argstr='--hemi %s', mandatory=True, desc='hemisphere of data')
+    transformed_file = File(name_template="%s_asVol.nii", desc='Output volume', argstr='--outvol %s',
+                            name_source=['source_file'], hash_files=False)
+    reg_file = File(exists=True, argstr='--volreg %s',
+                    mandatory=True,
+                    desc='tkRAS-to-tkRAS matrix   (tkregister2 format)',
+                    xor=['subject_id'])
+    template_file = File(exists=True, argstr='--template %s',
+                      desc='Output template volume')
+    mkmask = traits.Bool(desc='make a mask instead of loading surface values', argstr='--mkmask')
+    vertexvol_file = File(name_template="%s_asVol_vertex.nii", desc='Path name of the vertex output '
+                          'volume, which is the same as output volume except that the value of each '
+                          'voxel is the vertex-id that is mapped to that voxel.',
+                          argstr='--vtxvol %s', name_source=['source_file'], hash_files=False)
+    surf_name = traits.Str(exists=True, argstr='--surf %s',desc='surfname (default is white)')
+    projfrac = traits.Float(exists=True, argstr='--projfrac %s',desc='thickness fraction')
+    subjects_dir = traits.Str(argstr='--sd %s',desc='freesurfer subjects directory defaults to $SUBJECTS_DIR')
+    subject_id = traits.Str(argstr='--identity %s',desc='subject id', xor=['reg_file'])
+
+class Surface2VolTransformOutputSpec(TraitedSpec):
+    transformed_file = File(exists=True, desc='Path to output file if used normally')
+    vertexvol_file = File(desc='vertex map volume path id. Optional')
+
+class Surface2VolTransform(FSCommand):
+    """Use FreeSurfer mri_surf2vol to apply a transform.
+
+    Examples
+    --------
+
+    >>> from nipype.interfaces.freesurfer import Surface2VolTransform
+    >>> xfm2vol = Surface2VolTransform()
+    >>> xfm2vol.inputs.source_file = 'lh.cope1.mgz'
+    >>> xfm2vol.inputs.reg_file = 'register.mat'
+    >>> xfm2vol.inputs.hemi = 'lh'
+    >>> xfm2vol.inputs.template_file = 'cope1.nii.gz'
+    >>> xfm2vol.inputs.subjects_dir = '.'
+    >>> xfm2vol.cmdline
+    'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii'
+    >>> res = xfm2vol.run()# doctest: +SKIP
+
+    """
+
+    _cmd = 'mri_surf2vol'
+    input_spec = Surface2VolTransformInputSpec
+    output_spec = Surface2VolTransformOutputSpec
 
 class ApplyMaskInputSpec(FSTraitedSpec):