Updates for MRtrix FilterTracks interface

Author: Erik Ziegler

nipype/interfaces/mrtrix/__init__.py

@@ -1,6 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from .tracking import (Tracks2Prob, StreamlineTrack,
+from .tracking import (Tracks2Prob, FilterTracks, StreamlineTrack,
                        DiffusionTensorStreamlineTrack,
                        SphericallyDeconvolutedStreamlineTrack,
                        ProbabilisticSphericallyDeconvolutedStreamlineTrack)

nipype/interfaces/mrtrix/tracking.py

@@ -32,20 +32,20 @@ class FilterTracksInputSpec(CommandLineInputSpec):
 
     out_filename = File(genfile=True, argstr='%s', position=-1, desc='Output filtered track filename')
     no_mask_interpolation = traits.Bool(argstr='-nomaskinterp', desc="Turns off trilinear interpolation of mask images.")
-    invert = traits.Bool(argstr='-invert', desc="invert the matching process, so that tracks that would" /
+    invert = traits.Bool(argstr='-invert', desc="invert the matching process, so that tracks that would" \
                 "otherwise have been included are now excluded and vice-versa.")
 
 
     quiet = traits.Bool(argstr='-quiet', position=1, desc="Do not display information messages or progress status.")
     debug = traits.Bool(argstr='-debug', position=1, desc="Display debugging messages.")
 
 class FilterTracksOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='the output image of the major eigenvectors of the diffusion tensor image.')
+    out_file = File(exists=True, desc='the output filtered tracks')
 
 class FilterTracks(CommandLine):
     """
-    Use regions-of-interest to select a sub-set of tracks
-    from a given track file.
+    Use regions-of-interest to select a subset of tracks
+    from a given MRtrix track file.
 
     Example
     -------
@@ -62,21 +62,22 @@ class FilterTracks(CommandLine):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['out_file'] = self.inputs.out_filename
-        if not isdefined(outputs['out_file']):
-            outputs['out_file'] = op.abspath(self._gen_outfilename())
-        else:
-            outputs['out_file'] = op.abspath(outputs['out_file'])
+        outputs['out_file'] = op.abspath(self._gen_outfilename())
         return outputs
 
     def _gen_filename(self, name):
         if name is 'out_filename':
             return self._gen_outfilename()
         else:
             return None
+
     def _gen_outfilename(self):
-        _, name , _ = split_filename(self.inputs.in_file)
-        return name + '_filt.tck'
+        if isdefined(self.inputs.out_filename):
+            path, name , _ = split_filename(self.inputs.out_filename)
+            return op.join(path, name + '.tck')
+        else:
+            _, name , _ = split_filename(self.inputs.in_file)
+            return op.abspath(name + '_filt.tck')
 
 
 class Tracks2ProbInputSpec(CommandLineInputSpec):