Added BET's in_file conversion to relative path.

Author: ZviBaratz

nipype/interfaces/fsl/preprocess.py

@@ -165,10 +165,21 @@ def _run_interface(self, runtime):
             self.raise_exception(runtime)
         return runtime
 
+    def _format_arg(self, name, spec, value):
+        formatted = super(BET, self)._format_arg(name, spec, value)
+        if name == "in_file":
+            # Convert to relative path to prevent BET failure
+            # with long paths.
+            return op.relpath(formatted, start=os.getcwd())
+        return formatted
+
     def _gen_outfilename(self):
         out_file = self.inputs.out_file
+        # Generate default output filename if non specified.
         if not isdefined(out_file) and isdefined(self.inputs.in_file):
             out_file = self._gen_fname(self.inputs.in_file, suffix="_brain")
+            # Convert to relative path to prevent BET failure
+            # with long paths.
             return op.relpath(out_file, start=os.getcwd())
         return out_file