diff --git a/.travis.yml b/.travis.yml
index fe9bf96a93..fe17fe3398 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -23,6 +23,7 @@ before_install:
 - if $INSTALL_DEB_DEPENDECIES; then travis_retry sudo apt-get install -qq fsl-atlases;
   fi
 - if $INSTALL_DEB_DEPENDECIES; then source /etc/fsl/fsl.sh; fi
+- if $INSTALL_DEB_DEPENDECIES; then source /etc/afni/afni.sh; fi
 install:
 - conda update --yes conda
 - conda create -n testenv --yes pip python=$TRAVIS_PYTHON_VERSION
diff --git a/nipype/interfaces/afni/base.py b/nipype/interfaces/afni/base.py
index da77dc7728..22870d5d19 100644
--- a/nipype/interfaces/afni/base.py
+++ b/nipype/interfaces/afni/base.py
@@ -37,10 +37,30 @@ def version():
            Version number as string or None if AFNI not found
 
         """
-        clout = CommandLine(command='afni_vcheck',
-                            terminal_output='allatonce').run()
-        out = clout.runtime.stdout
-        return out.split('\n')[1]
+        try:
+            clout = CommandLine(command='afni_vcheck',
+                                terminal_output='allatonce').run()
+        except IOError:
+            # If afni_vcheck is not present, return None
+            warn('afni_vcheck executable not found.')
+            return None
+        except RuntimeError as e:
+            # If AFNI is outdated, afni_vcheck throws error
+            warn('AFNI is outdated')
+            return str(e).split('\n')[4].split('=', 1)[1].strip()
+
+        # Try to parse the version number
+        out = clout.runtime.stdout.split('\n')[1].split('=', 1)[1].strip()
+
+        if out.startswith('AFNI_'):
+            out = out[5:]
+
+        v = out.split('.')
+        try:
+            v = [int(n) for n in v]
+        except ValueError:
+            return out
+        return tuple(v)
 
     @classmethod
     def outputtype_to_ext(cls, outputtype):
@@ -160,3 +180,10 @@ def _list_outputs(self):
                     if ext == "":
                         outputs[name] = outputs[name] + "+orig.BRIK"
         return outputs
+
+
+def no_afni():
+    """ Checks if AFNI is available """
+    if Info.version() is None:
+        return True
+    return False
diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py
index 96bbaaccae..058a99a1af 100644
--- a/nipype/interfaces/afni/preprocess.py
+++ b/nipype/interfaces/afni/preprocess.py
@@ -1235,6 +1235,17 @@ class SkullStrip(AFNICommand):
     input_spec = SkullStripInputSpec
     output_spec = AFNICommandOutputSpec
 
+    def __init__(self, **inputs):
+        from .base import Info, no_afni
+        super(SkullStrip, self).__init__(**inputs)
+
+        if not no_afni():
+            v = Info.version()
+
+            # As of AFNI 16.0.00, redirect_x is not needed
+            if isinstance(v[0], int) and v[0] > 15:
+                self._redirect_x = False
+
 
 class TCatInputSpec(AFNICommandInputSpec):
     in_files = InputMultiPath(