Merge https://github.com/stymy/nipype

Conflicts:
	nipype/interfaces/afni/preprocess.py

Author: stymy

nipype/interfaces/afni/preprocess.py

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

nipype/interfaces/freesurfer/__init__.py

@@ -4,7 +4,7 @@
 
 from .base import Info, FSCommand
 from .preprocess import (ParseDICOMDir, UnpackSDICOMDir, MRIConvert, Resample,
-                         ReconAll, BBRegister, ApplyVolTransform, Smooth,
+                         ReconAll, BBRegister, ApplyVolTransform, Surface2VolTransform, Smooth,
                          DICOMConvert, RobustRegister, FitMSParams,
                          SynthesizeFLASH)
 from .model import (MRISPreproc, GLMFit, OneSampleTTest, Binarize, Concatenate,

nipype/interfaces/freesurfer/preprocess.py

@@ -1021,6 +1021,64 @@ 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',