diff --git a/fsl/utils/run.py b/fsl/utils/run.py
index 12cc036067d7c502afbca6cd90153c38ced00859..3c65cba856614a70ab0e16855e094d14b851bb9b 100644
--- a/fsl/utils/run.py
+++ b/fsl/utils/run.py
@@ -20,6 +20,7 @@
 
 
 import               sys
+import               shlex
 import               logging
 import               threading
 import               contextlib
@@ -81,7 +82,7 @@ def prepareArgs(args):
 
         # Argument was a command string
         if isinstance(args[0], six.string_types):
-            args = args[0].split()
+            args = shlex.split(args[0])
 
         # Argument was an unpacked sequence
         else: