Merge pull request #2529 from oesteban/enh/fslmaths-add-mas

oesteban · web-flow · commit dc09e00ad2c9 · 2018-04-04T09:11:59.000-07:00
[FIX] Add ``-mas`` argument to fsl.utils.ImageMaths
diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py
@@ -24,19 +24,20 @@ def test_ImageMaths_inputs():
             argstr='%s',
             position=3,
         ),
+        mask_file=dict(argstr='-mas %s', ),
         op_string=dict(
             argstr='%s',
             position=2,
         ),
         out_data_type=dict(
             argstr='-odt %s',
-            position=5,
+            position=-1,
         ),
         out_file=dict(
             argstr='%s',
             genfile=True,
             hash_files=False,
-            position=4,
+            position=-2,
         ),
         output_type=dict(),
         suffix=dict(),
diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py
@@ -500,7 +500,9 @@ def _list_outputs(self):
 class ImageMathsInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr="%s", mandatory=True, position=1)
     in_file2 = File(exists=True, argstr="%s", position=3)
-    out_file = File(argstr="%s", position=4, genfile=True, hash_files=False)
+    mask_file = File(exists=True, argstr='-mas %s',
+                     desc='use (following image>0) to mask current image')
+    out_file = File(argstr="%s", position=-2, genfile=True, hash_files=False)
     op_string = traits.Str(
         argstr="%s",
         position=2,
@@ -514,7 +516,7 @@ class ImageMathsInputSpec(FSLCommandInputSpec):
         'double',
         'input',
         argstr="-odt %s",
-        position=5,
+        position=-1,
         desc=("output datatype, one of (char, short, "
               "int, float, double, input)"))
 
