update dwidenoise, mrdegibbs and dwibiascorrect

Author: josephmje

nipype/interfaces/mrtrix3/preprocess.py

@@ -100,19 +100,16 @@ class MRDeGibbsInputSpec(MRTrix3BaseInputSpec):
         desc='indicate the plane in which the data was acquired (axial = 0,1; '
              'coronal = 0,2; sagittal = 1,2')
     nshifts = traits.Int(
-        default_value=20,
-        usedefault=True,
+        20,
         argstr='-nshifts %d',
         desc='discretization of subpixel spacing (default = 20)')
     minW = traits.Int(
-        default_value=1,
-        usedefault=True,
+        1,
         argstr='-minW %d',
         desc='left border of window used for total variation (TV) computation '
              '(default = 1)')
     maxW = traits.Int(
-        default_value=3,
-        usedefault=True,
+        3,
         argstr='-maxW %d',
         desc='right border of window used for total variation (TV) computation '
              '(default = 3)')
@@ -159,7 +156,7 @@ class MRDeGibbs(MRTrix3Base):
     >>> unring = mrt.MRDeGibbs()
     >>> unring.inputs.in_file = 'dwi.mif'
     >>> unring.cmdline
-    'mrdegibbs -axes 0,1 -maxW 3 -minW 1 -nshifts 20 dwi.mif dwi_unr.mif'
+    'mrdegibbs dwi.mif dwi_unr.mif'
     >>> unring.run()                                 # doctest: +SKIP
     """
 

nipype/interfaces/mrtrix3/tests/test_auto_MRDeGibbs.py

@@ -11,7 +11,6 @@ def test_MRDeGibbs_inputs():
             maxlen=2,
             minlen=2,
             sep=',',
-            usedefault=True,
         ),
         bval_scale=dict(argstr='-bvalue_scaling %s', ),
         environ=dict(
@@ -38,18 +37,9 @@ def test_MRDeGibbs_inputs():
             mandatory=True,
             position=-2,
         ),
-        maxW=dict(
-            argstr='-maxW %d',
-            usedefault=True,
-        ),
-        minW=dict(
-            argstr='-minW %d',
-            usedefault=True,
-        ),
-        nshifts=dict(
-            argstr='-nshifts %d',
-            usedefault=True,
-        ),
+        maxW=dict(argstr='-maxW %d', ),
+        minW=dict(argstr='-minW %d', ),
+        nshifts=dict(argstr='-nshifts %d', ),
         nthreads=dict(
             argstr='-nthreads %d',
             nohash=True,