Merge pull request #2065 from juhuntenburg/fix/cbstools_params

FIX adapting mp2rage masking interface to new parameter names in cbstools 3

Author: satra

README.rst

@@ -33,7 +33,7 @@ NIPYPE: Neuroimaging in Python: Pipelines and Interfaces
 .. image:: https://img.shields.io/badge/gitter-join%20chat%20%E2%86%92-brightgreen.svg?style=flat
     :target: http://gitter.im/nipy/nipype
     :alt: Chat
-    
+
 .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.581704.svg
    :target: https://doi.org/10.5281/zenodo.581704
 

nipype/interfaces/mipav/developer.py

@@ -722,10 +722,10 @@ class JistIntensityMp2rageMaskingInputSpec(CommandLineInputSpec):
     inSkip = traits.Enum("true", "false", desc="Skip zero values", argstr="--inSkip %s")
     inMasking = traits.Enum("binary", "proba", desc="Whether to use a binary threshold or a weighted average based on the probability.", argstr="--inMasking %s")
     xPrefExt = traits.Enum("nrrd", desc="Output File Type", argstr="--xPrefExt %s")
-    outSignal = traits.Either(traits.Bool, File(), hash_files=False, desc="Signal Proba Image", argstr="--outSignal %s")
-    outSignal2 = traits.Either(traits.Bool, File(), hash_files=False, desc="Signal Mask Image", argstr="--outSignal2 %s")
-    outMasked = traits.Either(traits.Bool, File(), hash_files=False, desc="Masked T1 Map Image", argstr="--outMasked %s")
-    outMasked2 = traits.Either(traits.Bool, File(), hash_files=False, desc="Masked Iso Image", argstr="--outMasked2 %s")
+    outSignal = traits.Either(traits.Bool, File(), hash_files=False, desc="Signal Proba Image", argstr="--outSignal_Proba %s")
+    outSignal2 = traits.Either(traits.Bool, File(), hash_files=False, desc="Signal Mask Image", argstr="--outSignal_Mask %s")
+    outMasked = traits.Either(traits.Bool, File(), hash_files=False, desc="Masked T1 Map Image", argstr="--outMasked_T1_Map %s")
+    outMasked2 = traits.Either(traits.Bool, File(), hash_files=False, desc="Masked Iso Image", argstr="--outMasked_T1weighted %s")
     null = traits.Str(desc="Execution Time", argstr="--null %s")
     xDefaultMem = traits.Int(desc="Set default maximum heap size", argstr="-xDefaultMem %d")
     xMaxProcess = traits.Int(1, desc="Set default maximum number of processes.", argstr="-xMaxProcess %d", usedefault=True)

nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py

@@ -26,16 +26,16 @@ def test_JistIntensityMp2rageMasking_inputs():
     ),
     null=dict(argstr='--null %s',
     ),
-    outMasked=dict(argstr='--outMasked %s',
+    outMasked=dict(argstr='--outMasked_T1_Map %s',
     hash_files=False,
     ),
-    outMasked2=dict(argstr='--outMasked2 %s',
+    outMasked2=dict(argstr='--outMasked_T1weighted %s',
     hash_files=False,
     ),
-    outSignal=dict(argstr='--outSignal %s',
+    outSignal=dict(argstr='--outSignal_Proba %s',
     hash_files=False,
     ),
-    outSignal2=dict(argstr='--outSignal2 %s',
+    outSignal2=dict(argstr='--outSignal_Mask %s',
     hash_files=False,
     ),
     terminal_output=dict(nohash=True,