diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 8bf4c456d2..bf73335d8f 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -880,24 +880,29 @@ def get_dependencies(name, environ):
     Uses otool on darwin, ldd on linux. Currently doesn't support windows.
 
     """
+    command = None
     if sys.platform == 'darwin':
-        proc = sp.Popen(
-            'otool -L `which %s`' % name,
-            stdout=sp.PIPE,
-            stderr=sp.PIPE,
-            shell=True,
-            env=environ)
+        command = 'otool -L `which %s`' % name
     elif 'linux' in sys.platform:
+        command = 'ldd `which %s`' % name
+    else:
+        return 'Platform %s not supported' % sys.platform
+
+    deps = None
+    try:
         proc = sp.Popen(
-            'ldd `which %s`' % name,
+            command,
             stdout=sp.PIPE,
             stderr=sp.PIPE,
             shell=True,
             env=environ)
-    else:
-        return 'Platform %s not supported' % sys.platform
-    o, e = proc.communicate()
-    return o.rstrip()
+        o, e = proc.communicate()
+        deps = o.rstrip()
+    except Exception as ex:
+        deps = '"%s" failed' % command
+        fmlogger.warning('Could not get dependencies of %s. Error:\n%s',
+                         name, ex.message)
+    return deps
 
 
 def canonicalize_env(env):