Merge pull request #453 from chrisfilo/enh/fslreorient

Added reorient2std interface

Author: chrisgorgo

nipype/interfaces/fsl/__init__.py

@@ -15,7 +15,7 @@
 from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
-                    SwapDimensions, PowerSpectrum)
+                    SwapDimensions, PowerSpectrum, Reorient2Std)
 from .dti import (EddyCorrect, BEDPOSTX, DTIFit, ProbTrackX, VecReg, ProjThresh,
                   FindTheBiggest, DistanceMap, TractSkeleton, XFibres,
                   MakeDyadicVectors)

nipype/interfaces/fsl/utils.py

@@ -1151,3 +1151,39 @@ def _list_outputs(self):
             outputs['exf_mask'] = self._gen_fname(cwd=self.inputs.tmpdir,
                                                   basename='maskexf')
         return outputs
+    
+class Reorient2StdInputSpec(FSLCommandInputSpec):
+    in_file = File(exists=True, mandatory=True, argstr="%s")
+    out_file = File(genfile=True, hash_files=False, argstr="%s")
+    
+class Reorient2StdOutputSpec(TraitedSpec):
+    out_file = File(exists=True)
+    
+class Reorient2Std(FSLCommand):
+    """fslreorient2std is a tool for reorienting the image to match the
+    approximate orientation of the standard template images (MNI152).
+
+    Examples
+    --------
+    >>> reorient = Reorient2Std()
+    >>> reorient.inputs.in_file = "functional.nii"
+    >>> res = reorient.run() # doctest: +SKIP
+
+
+    """
+    _cmd = 'fslreorient2std'
+    input_spec = Reorient2StdInputSpec
+    output_spec = Reorient2StdOutputSpec
+
+    def _gen_filename(self, name):
+        if name == 'out_file':
+            return self._gen_fname(self.inputs.in_file,
+                                  suffix="_reoriented")
+        return None
+    
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        if not isdefined(self.inputs.out_file):
+            outputs['out_file'] = self._gen_filename('out_file')
+        else:
+            outputs['out_file'] = os.path.abspath(self.inputs.out_file)