FIX: Ensures 'out_file' of MRIsConvert is an absolute path.

This commit ensures that 'out_file' of MRIsConvert is an absolute path.
MRIsConvert requires an absolute path or a path beginning with "./". This
commit also ensures that either out_file or out_datatype are defined.

Author: David Ellis

nipype/interfaces/freesurfer/utils.py

@@ -814,10 +814,12 @@ class MRIsConvertInputSpec(FSTraitedSpec):
     origname = traits.String(argstr="-o %s", desc="read orig positions")
 
     in_file = File(exists=True, mandatory=True, position=-2, argstr='%s', desc='File to read/convert')
-    out_file = File(argstr='%s', position=-1, genfile=True, xor=['out_datatype'],
+    out_file = File(argstr='%s', position=-1, genfile=True,
+                    xor=['out_datatype'], mandatory=True,
                     desc='output filename or True to generate one')
 
-    out_datatype = traits.Enum("ico", "tri", "stl", "vtk", "gii", "mgh", "mgz", xor=['out_file'],
+    out_datatype = traits.Enum("ico", "tri", "stl", "vtk", "gii", "mgh", "mgz",
+                               xor=['out_file'], mandatory=True,
                                desc="These file formats are supported:  ASCII:       .asc"
                                "ICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume': .mgh, .mgz")
 
@@ -846,6 +848,11 @@ class MRIsConvert(FSCommand):
     input_spec = MRIsConvertInputSpec
     output_spec = MRIsConvertOutputSpec
 
+    def _format_arg(self, name, spec, value):
+        if name == "out_file" and not os.path.isabs(value):
+            value = os.path.abspath(value)
+        return super(MRIsConvert, self)._format_arg(name, spec, value)
+    
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs["converted"] = os.path.abspath(self._gen_outfilename())