Merge branch 'master' of https://github.com/nipy/nipype.git

Author: chrisgorgo

.gitignore

@@ -12,3 +12,4 @@
 .project
 .settings
 .pydevproject
+.idea/

nipype/interfaces/fsl/preprocess.py

@@ -1197,7 +1197,7 @@ class FUGUEInputSpec(FSLCommandInputSpec):
                                desc='apply Fourier (sinusoidal) fitting of order N')
     pava = traits.Bool(argstr='--pava',
                        desc='apply monotonic enforcement via PAVA')
-    despike_theshold = traits.Float(argstr='--despikethreshold=%s',
+    despike_threshold = traits.Float(argstr='--despikethreshold=%s',
                                     desc='specify the threshold for de-spiking (default=3.0)')
     unwarp_direction = traits.Enum('x', 'y', 'z', 'x-', 'y-', 'z-',
                                    argstr='--unwarpdir=%s',
@@ -1287,13 +1287,13 @@ def _parse_inputs(self, skip=None):
                 self.inputs.shift_out_file = self._gen_fname(
                     self.inputs.in_file, suffix='_vsm')
 
-        if self.inputs.forward_warping or not isdefined(self.inputs.in_file):
-            skip += ['unwarped_file']
+        if not isdefined(self.inputs.in_file):
+            skip += ['unwarped_file', 'warped_file']
+        elif self.inputs.forward_warping:
             if not isdefined(self.inputs.warped_file):
                 self.inputs.warped_file = self._gen_fname(
                     self.inputs.in_file, suffix='_warped')
-        if not self.inputs.forward_warping or not isdefined(self.inputs.in_file):
-            skip += ['warped_file']
+        elif not self.inputs.forward_warping:
             if not isdefined(self.inputs.unwarped_file):
                 self.inputs.unwarped_file = self._gen_fname(
                     self.inputs.in_file, suffix='_unwarped')

nipype/interfaces/fsl/tests/test_auto_FUGUE.py

@@ -61,13 +61,13 @@ def test_FUGUE_inputs():
     nohash=True,
     ),
     output_type=dict(),
-    despike_theshold=dict(argstr='--despikethreshold=%s',
-    ),
     icorr=dict(requires=['shift_in_file'],
     argstr='--icorr',
     ),
     fmap_in_file=dict(argstr='--loadfmap=%s',
     ),
+    despike_threshold=dict(argstr='--despikethreshold=%s',
+    ),
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     fmap_out_file=dict(hash_files=False,