[ENH] Implement missing inputs/outputs in avscale

Author: oesteban

nipype/interfaces/fsl/__init__.py

@@ -12,7 +12,7 @@
 from .model import (Level1Design, FEAT, FEATModel, FILMGLS, FEATRegister,
                     FLAMEO, ContrastMgr, MultipleRegressDesign, L2Model, SMM,
                     MELODIC, SmoothEstimate, Cluster, Randomise, GLM)
-from .utils import (Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
+from .utils import (AvScale, Smooth, Merge, ExtractROI, Split, ImageMaths, ImageMeants,
                     ImageStats, FilterRegressor, Overlay, Slicer,
                     PlotTimeSeries, PlotMotionParams, ConvertXFM,
                     SwapDimensions, PowerSpectrum, Reorient2Std,

nipype/interfaces/fsl/utils.py

@@ -609,8 +609,11 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
 
 
 class AvScaleInputSpec(FSLCommandInputSpec):
-    mat_file = File(exists=True, argstr="%s",
-                    desc='mat file to read', position=0)
+    all_param = traits.Bool(False, argstr='--allparams')
+    mat_file = File(exists=True, argstr='%s',
+                    desc='mat file to read', position=-2)
+    ref_file = File(exists=True, argstr='%s', position=-1,
+                    desc='reference file to get center of rotation')
 
 
 class AvScaleOutputSpec(TraitedSpec):