fixed gradient nonlinearities implementation

Author: oesteban

nipype/interfaces/fsl/dti.py

@@ -101,8 +101,8 @@ def _list_outputs(self):
 
 
 class BEDPOSTXInputSpec(FSLXCommandInputSpec):
-    gradnonlin = File(exists=True, argstr='--gradnonlin=%s',
-                      desc='consider gradient nonlinearities, default off')
+    gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient '
+                             'nonlinearities, default off'))
 
 
 class BEDPOSTX(FSLXCommand):
@@ -138,12 +138,18 @@ class BEDPOSTX(FSLXCommand):
     _can_resume = True
 
 
+class XFibresInputSpec(FSLXCommandInputSpec):
+    gradnonlin = File(exists=True, argstr='--gradnonlin=%s',
+                      desc='gradient file corresponding to slice')
+
+
 class XFibres(FSLXCommand):
     """
-    Perform model parameters estimation for local (voxelwise) diffusion parameters
+    Perform model parameters estimation for local (voxelwise) diffusion
+    parameters
     """
     _cmd = 'xfibres'
-    input_spec = FSLXCommandInputSpec
+    input_spec = XFibresInputSpec
     output_spec = FSLXCommandOutputSpec
 
 

nipype/interfaces/fsl/tests/test_auto_BEDPOSTX.py

@@ -38,7 +38,7 @@ def test_BEDPOSTX_inputs():
     ),
     fudge=dict(argstr='--fudge=%d',
     ),
-    gradnonlin=dict(argstr='--gradnonlin=%s',
+    gradnonlin=dict(argstr='-g',
     ),
     ignore_exception=dict(nohash=True,
     usedefault=True,

nipype/interfaces/fsl/tests/test_auto_XFibres.py

@@ -38,6 +38,8 @@ def test_XFibres_inputs():
     ),
     fudge=dict(argstr='--fudge=%d',
     ),
+    gradnonlin=dict(argstr='--gradnonlin=%s',
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),