Repository: nipy/nipype

Issue:
JistIntensityMp2rageMasking interface incompatible with current CBS Tools release
For the command underlying the interface mipav.JistIntensityMp2rageMasking the parameter names have changed in the current CBS Tools release, which makes the interface fail. I meant to do a PR but then saw the mipav/developer.py file is autogenerated and should not be be edited. 

These would be the required changes:
https://github.com/nipy/nipype/compare/master...juhuntenburg:fix/cbstools_params


Comments:

Patch:
diff --git a/README.rst b/README.rst
index aa41f34d6..5064198dd 100644
--- a/README.rst
+++ b/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
 
diff --git a/nipype/interfaces/mipav/developer.py b/nipype/interfaces/mipav/developer.py
index ac42f7c5a..141a7de1c 100644
--- a/nipype/interfaces/mipav/developer.py
+++ b/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)


Test patch:
diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py
index 95700af1b..0fd3ed52e 100644
--- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py
+++ b/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,