fixed pull request issues:

wrapping Surface2VolTransform,
-moved from preprocess.py to utils.py
-improved input descriptions
-renamed output suffix

Author: stymy

nipype/interfaces/afni/preprocess.py

@@ -329,8 +329,7 @@ class AutoTcorrelateInputSpec(AFNICommandInputSpec):
                 argstr="-mask %s")
     mask_only_targets = traits.Bool(desc="use mask only on targets voxels",
                                     argstr="-mask_only_targets",
-                                    xor=['mask_source'])
-                                    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, Surface2VolTransform, 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')
 
@@ -1021,65 +1020,6 @@ def _gen_filename(self, name):
             return self._get_outfile()
         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',desc='hemisphere of data')
-    transformed_file = File(desc='Output volume', argstr='--outvol %s', genfile=True)
-    reg_file = File(exists=True, argstr='--volreg %s',
-                    mandatory=True,
-                    desc='tkRAS-to-tkRAS matrix   (tkregister2 format)') 
-    template_file = File(exists=True, argstr='--template %s',
-                      desc='Output template volume')
-    mkmask = traits.Bool(desc='make a mask instead of loading surfval', argstr='--mkmask')
-    vertexvol_file = File(desc='vertex map volume path id', argstr='--vtxvol %s', genfile=True)
-    surf_file = File(exists=True, argstr='--surf %s',desc='surfname (default is white)')
-    projfrac_file = File(exists=True, argstr='--projfrac %s',desc='thickness fraction')
-    subjects_dir = traits.Str(argstr='--sd %s',desc='freesurfer subjects directory defaults to $SUBJECTS_DIR')
-    identity = traits.Str(argstr='--identity %s',desc='use identity (must supply subject name)')
-
-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 = 'surface.nii'
-    >>> xfm2vol.inputs.reg_file = 'register.dat'
-    >>> xfm2vol.inputs.hemi = 'lh'
-    >>> xfm2vol.cmdline
-    'mri_surf2vol --volreg register.dat --surfval structural.nii --hemi lh'
-
-    """
-
-    _cmd = 'mri_surf2vol'
-    input_spec = Surface2VolTransformInputSpec
-    output_spec = Surface2VolTransformOutputSpec
-
-    def _get_outfile(self):
-        outfile = self.inputs.transformed_file
-        if not isdefined(outfile):
-            outfile = self._gen_fname(self.inputs.source_file,
-                                      suffix='_xfm2vol')
-        return outfile
-
-    def _list_outputs(self):
-        outputs = self.output_spec().get()
-        outputs['transformed_file'] = self._get_outfile()
-        return outputs
-
-    def _gen_filename(self, name):
-        if name == 'transformed_file':
-            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/utils.py

@@ -382,6 +382,65 @@ 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',desc='hemisphere of data')
+    transformed_file = File(desc='Output volume', argstr='--outvol %s', genfile=True)
+    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(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', genfile=True)
+    surf_file = File(exists=True, argstr='--surf %s',desc='surfname (default is white)')
+    projfrac_file = 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 = 'surface.nii'
+    >>> xfm2vol.inputs.reg_file = 'register.dat'
+    >>> xfm2vol.inputs.hemi = 'lh'
+    >>> xfm2vol.cmdline
+    'mri_surf2vol --volreg register.dat --surfval surface.nii --hemi lh'
+
+    """
+
+    _cmd = 'mri_surf2vol'
+    input_spec = Surface2VolTransformInputSpec
+    output_spec = Surface2VolTransformOutputSpec
+
+    def _get_outfile(self):
+        outfile = self.inputs.transformed_file
+        if not isdefined(outfile):
+            outfile = self._gen_fname(self.inputs.source_file,
+                                      suffix='_asVol')
+        return outfile
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['transformed_file'] = self._get_outfile()
+        return outputs
+
+    def _gen_filename(self, name):
+        if name == 'transformed_file':
+            return self._get_outfile()
+        return None
 
 class ApplyMaskInputSpec(FSTraitedSpec):