Merge pull request #750 from mluessi/fix_topup

FIX: topup out_base and params

Author: satra

nipype/interfaces/fsl/epi.py

@@ -169,7 +169,9 @@ def _parse_inputs( self, skip=None ):
             skip = []
 
         if not isdefined(self.inputs.out_base ):
-            self.inputs.out_base = os.path.abspath( './nipypetu' )
+            self.inputs.out_base = './nipypetu'
+
+        self.inputs.out_base = os.path.abspath(self.inputs.out_base)
 
         if isdefined( self.inputs.encoding_file ):
             skip.append( 'encoding_direction' )
@@ -238,8 +240,8 @@ class ApplyTOPUPInputSpec( FSLCommandInputSpec ):
     in_topup = File( mandatory=True, desc='basename of field/movements (from topup)', argstr='--topup=%s' )
 
     out_base = File( desc='basename for output (warped) image', argstr='--out=%s' )
-    method = traits.Enum( ('jac','lsr'), argstr='-m=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
-    interp = traits.Enum( ('trilinear','spline'), argstr='-n=%s', desc='interpolation method' )
+    method = traits.Enum( ('jac','lsr'), argstr='--method=%s', desc='use jacobian modulation (jac) or least-squares resampling (lsr)' )
+    interp = traits.Enum( ('trilinear','spline'), argstr='--interp=%s', desc='interpolation method' )
     datatype = traits.Enum( ('char', 'short', 'int', 'float', 'double' ), argstr='-d=%s', desc='force output data type' )
 
 
@@ -289,7 +291,9 @@ def _parse_inputs( self, skip=None ):
             skip = []
 
         if not isdefined(self.inputs.out_base ):
-            self.inputs.out_base = os.path.abspath( './nipypeatu' )
+            self.inputs.out_base = './nipypeatu'
+
+        self.inputs.out_base = os.path.abspath(self.inputs.out_base)
         return super(ApplyTOPUP, self)._parse_inputs(skip=skip)
 
 

nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py

@@ -12,7 +12,7 @@ def test_ApplyTOPUP_inputs():
     ),
     args=dict(argstr='%s',
     ),
-    interp=dict(argstr='-n=%s',
+    interp=dict(argstr='--interp=%s',
     ),
     in_files=dict(mandatory=True,
     argstr='%s',
@@ -32,7 +32,7 @@ def test_ApplyTOPUP_inputs():
     out_base=dict(argstr='--out=%s',
     ),
     output_type=dict(),
-    method=dict(argstr='-m=%s',
+    method=dict(argstr='--method=%s',
     ),
     )
     inputs = ApplyTOPUP.input_spec()