diff --git a/CHANGES b/CHANGES
index fc37efb061..8720078b98 100644
--- a/CHANGES
+++ b/CHANGES
@@ -29,6 +29,7 @@ Upcoming release 0.13
 * ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
 * ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
        (https://github.com/nipy/nipype/pull/1654)
+* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 
 Release 0.12.1 (August 3, 2016)
 ===============================
diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py
index ecced01676..2953963149 100644
--- a/nipype/interfaces/freesurfer/preprocess.py
+++ b/nipype/interfaces/freesurfer/preprocess.py
@@ -21,8 +21,8 @@
 import numpy as np
 from nibabel import load
 
-from ... import logging
-from ...utils.filemanip import fname_presuffix
+from ... import logging, LooseVersion
+from ...utils.filemanip import fname_presuffix, check_depends
 from ..io import FreeSurferSource
 from ..base import (TraitedSpec, File, traits,
                     Directory, InputMultiPath,
@@ -30,12 +30,20 @@
                     CommandLineInputSpec, isdefined)
 from .base import (FSCommand, FSTraitedSpec,
                    FSTraitedSpecOpenMP,
-                   FSCommandOpenMP)
+                   FSCommandOpenMP, Info)
 from .utils import copy2subjdir
 
 __docformat__ = 'restructuredtext'
 iflogger = logging.getLogger('interface')
 
+FSVersion = "0"
+_ver = Info.version()
+if _ver:
+    if 'dev' in _ver:
+        FSVersion = _ver.rstrip().split('-')[-1] + '.dev'
+    else:
+        FSVersion = _ver.rstrip().split('-v')[-1]
+
 
 class ParseDICOMDirInputSpec(FSTraitedSpec):
     dicom_dir = Directory(exists=True, argstr='--d %s', mandatory=True,
@@ -622,6 +630,8 @@ class ReconAllInputSpec(CommandLineInputSpec):
                          desc='Use converted T2 to refine the cortical surface')
     openmp = traits.Int(argstr="-openmp %d",
                         desc="Number of processors to use in parallel")
+    parallel = traits.Bool(argstr="-parallel",
+                           desc="Enable parallel execution")
     subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,
                              desc='path to subjects directory', genfile=True)
     flags = traits.Str(argstr='%s', desc='additional parameters')
@@ -656,85 +666,173 @@ class ReconAll(CommandLine):
     output_spec = ReconAllOutputSpec
     _can_resume = True
 
-    _steps = [
-        # autorecon1
-        ('motioncor', ['mri/rawavg.mgz', 'mri/orig.mgz']),
-        ('talairach', ['mri/transforms/talairach.auto.xfm',
-                       'mri/transforms/talairach.xfm']),
-        ('nuintensitycor', ['mri/nu.mgz']),
-        ('normalization', ['mri/T1.mgz']),
-        ('skullstrip',
-         ['mri/brainmask.auto.mgz',
-          'mri/brainmask.mgz']),
-        # autorecon2
-        ('gcareg', ['mri/transforms/talairach.lta']),
-        ('canorm', ['mri/norm.mgz']),
-        ('careg', ['mri/transforms/talairach.m3z']),
-        ('careginv', ['mri/transforms/talairach.m3z.inv.x.mgz',
-                      'mri/transforms/talairach.m3z.inv.y.mgz',
-                      'mri/transforms/talairach.m3z.inv.z.mgz']),
-        ('rmneck', ['mri/nu_noneck.mgz']),
-        ('skull-lta', ['mri/transforms/talairach_with_skull_2.lta']),
-        ('calabel',
-         ['mri/aseg.auto_noCCseg.mgz', 'mri/aseg.auto.mgz', 'mri/aseg.mgz']),
-        ('normalization2', ['mri/brain.mgz']),
-        ('maskbfs', ['mri/brain.finalsurfs.mgz']),
-        ('segmentation', ['mri/wm.asegedit.mgz', 'mri/wm.mgz']),
-        ('fill', ['mri/filled.mgz']),
-        ('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix']),
-        ('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix']),
-        ('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix']),
-        ('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix']),
-        ('fix', ['surf/lh.orig', 'surf/rh.orig']),
-        ('white',
-         ['surf/lh.white',
-          'surf/rh.white',
-          'surf/lh.curv',
-          'surf/rh.curv',
-          'surf/lh.area',
-          'surf/rh.area',
-          'label/lh.cortex.label',
-          'label/rh.cortex.label']),
-        ('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm']),
-        ('inflate2',
-         ['surf/lh.inflated',
-          'surf/rh.inflated',
-          'surf/lh.sulc',
-          'surf/rh.sulc',
-          'surf/lh.inflated.H',
-          'surf/rh.inflated.H',
-          'surf/lh.inflated.K',
-          'surf/rh.inflated.K']),
-        # autorecon3
-        ('sphere', ['surf/lh.sphere', 'surf/rh.sphere']),
-        ('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg']),
-        ('jacobian_white', ['surf/lh.jacobian_white',
-                            'surf/rh.jacobian_white']),
-        ('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv']),
-        ('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot']),
-        ('pial',
-         ['surf/lh.pial',
-          'surf/rh.pial',
-          'surf/lh.curv.pial',
-          'surf/rh.curv.pial',
-          'surf/lh.area.pial',
-          'surf/rh.area.pial',
-          'surf/lh.thickness',
-          'surf/rh.thickness']),
-        ('cortparc2', ['label/lh.aparc.a2009s.annot',
-                       'label/rh.aparc.a2009s.annot']),
-        ('parcstats2',
-         ['stats/lh.aparc.a2009s.stats',
-          'stats/rh.aparc.a2009s.stats',
-          'stats/aparc.annot.a2009s.ctab']),
-        ('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
-                        'mri/ribbon.mgz']),
-        ('segstats', ['stats/aseg.stats']),
-        ('aparc2aseg', ['mri/aparc+aseg.mgz', 'mri/aparc.a2009s+aseg.mgz']),
-        ('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats']),
-        ('balabels', ['BA.ctab', 'BA.thresh.ctab']),
-        ('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
-                             'label/rh.entorhinal_exvivo.label'])]
+    # Steps are based off of the recon-all tables [0,1] describing, inputs,
+    # commands, and outputs of each step of the recon-all process,
+    # controlled by flags.
+    #
+    # Each step is a 3-tuple containing (flag, [outputs], [inputs])
+    # A step is considered complete if all of its outputs exist and are newer
+    # than the inputs. An empty input list indicates input mtimes will not
+    # be checked. This may need updating, if users are working with manually
+    # edited files.
+    #
+    # [0] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
+    # [1] https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0
+    _autorecon1_steps = [
+        ('motioncor', ['mri/rawavg.mgz', 'mri/orig.mgz'], []),
+        ('talairach', ['mri/orig_nu.mgz',
+                       'mri/transforms/talairach.auto.xfm',
+                       'mri/transforms/talairach.xfm',
+                       # 'mri/transforms/talairach_avi.log',
+                       ], []),
+        ('nuintensitycor', ['mri/nu.mgz'], []),
+        ('normalization', ['mri/T1.mgz'], []),
+        ('skullstrip', ['mri/talairach_with_skull.lta',
+                        'mri/brainmask.auto.mgz',
+                        'mri/brainmask.mgz'], []),
+        ]
+    if LooseVersion(FSVersion) < LooseVersion("6.0.0"):
+        _autorecon2_steps = [
+            ('gcareg', ['mri/transforms/talairach.lta'], []),
+            ('canorm', ['mri/norm.mgz'], []),
+            ('careg', ['mri/transforms/talairach.m3z'], []),
+            ('careginv', ['mri/transforms/talairach.m3z.inv.x.mgz',
+                          'mri/transforms/talairach.m3z.inv.y.mgz',
+                          'mri/transforms/talairach.m3z.inv.z.mgz',
+                          ], []),
+            ('rmneck', ['mri/nu_noneck.mgz'], []),
+            ('skull-lta', ['mri/transforms/talairach_with_skull_2.lta'], []),
+            ('calabel', ['mri/aseg.auto_noCCseg.mgz',
+                         'mri/aseg.auto.mgz',
+                         'mri/aseg.mgz'], []),
+            ('normalization2', ['mri/brain.mgz'], []),
+            ('maskbfs', ['mri/brain.finalsurfs.mgz'], []),
+            ('segmentation', ['mri/wm.seg.mgz',
+                              'mri/wm.asegedit.mgz',
+                              'mri/wm.mgz'], []),
+            ('fill', ['mri/filled.mgz',
+                      # 'scripts/ponscc.cut.log',
+                      ], []),
+            ('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
+            ('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
+             []),
+            ('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
+             []),
+            ('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
+             []),
+            ('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
+            ('white', ['surf/lh.white', 'surf/rh.white',
+                       'surf/lh.curv', 'surf/rh.curv',
+                       'surf/lh.area', 'surf/rh.area',
+                       'label/lh.cortex.label', 'label/rh.cortex.label'], []),
+            ('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
+            ('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
+                          'surf/lh.sulc', 'surf/rh.sulc',
+                          'surf/lh.inflated.H', 'surf/rh.inflated.H',
+                          'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
+            ]
+        _autorecon3_steps = [
+            ('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
+            ('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
+            ('jacobian_white', ['surf/lh.jacobian_white',
+                                'surf/rh.jacobian_white'], []),
+            ('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
+            ('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
+            ('pial', ['surf/lh.pial', 'surf/rh.pial',
+                      'surf/lh.curv.pial', 'surf/rh.curv.pial',
+                      'surf/lh.area.pial', 'surf/rh.area.pial',
+                      'surf/lh.thickness', 'surf/rh.thickness'], []),
+            ('cortparc2', ['label/lh.aparc.a2009s.annot',
+                           'label/rh.aparc.a2009s.annot'], []),
+            ('parcstats2', ['stats/lh.aparc.a2009s.stats',
+                            'stats/rh.aparc.a2009s.stats',
+                            'stats/aparc.annot.a2009s.ctab'], []),
+            ('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
+                            'mri/ribbon.mgz'], []),
+            ('segstats', ['stats/aseg.stats'], []),
+            ('aparc2aseg', ['mri/aparc+aseg.mgz',
+                            'mri/aparc.a2009s+aseg.mgz'], []),
+            ('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats'], []),
+            ('balabels', ['BA.ctab', 'BA.thresh.ctab'], []),
+            ('label-exvivo-ec', ['label/lh.entorhinal_exvivo.label',
+                                 'label/rh.entorhinal_exvivo.label'], []),
+            ]
+    else:
+        _autorecon2_steps = [
+            ('gcareg', ['mri/transforms/talairach.lta'], []),
+            ('canorm', ['mri/norm.mgz'], []),
+            ('careg', ['mri/transforms/talairach.m3z'], []),
+            ('calabel', ['mri/aseg.auto_noCCseg.mgz',
+                         'mri/aseg.auto.mgz',
+                         'mri/aseg.mgz'], []),
+            ('normalization2', ['mri/brain.mgz'], []),
+            ('maskbfs', ['mri/brain.finalsurfs.mgz'], []),
+            ('segmentation', ['mri/wm.seg.mgz',
+                              'mri/wm.asegedit.mgz',
+                              'mri/wm.mgz'], []),
+            ('fill', ['mri/filled.mgz',
+                      # 'scripts/ponscc.cut.log',
+                      ], []),
+            ('tessellate', ['surf/lh.orig.nofix', 'surf/rh.orig.nofix'], []),
+            ('smooth1', ['surf/lh.smoothwm.nofix', 'surf/rh.smoothwm.nofix'],
+             []),
+            ('inflate1', ['surf/lh.inflated.nofix', 'surf/rh.inflated.nofix'],
+             []),
+            ('qsphere', ['surf/lh.qsphere.nofix', 'surf/rh.qsphere.nofix'],
+             []),
+            ('fix', ['surf/lh.orig', 'surf/rh.orig'], []),
+            ('white', ['surf/lh.white.preaparc', 'surf/rh.white.preaparc',
+                       'surf/lh.curv', 'surf/rh.curv',
+                       'surf/lh.area', 'surf/rh.area',
+                       'label/lh.cortex.label', 'label/rh.cortex.label'], []),
+            ('smooth2', ['surf/lh.smoothwm', 'surf/rh.smoothwm'], []),
+            ('inflate2', ['surf/lh.inflated', 'surf/rh.inflated',
+                          'surf/lh.sulc', 'surf/rh.sulc'], []),
+            ('curvHK', ['surf/lh.white.H', 'surf/rh.white.H',
+                        'surf/lh.white.K', 'surf/rh.white.K',
+                        'surf/lh.inflated.H', 'surf/rh.inflated.H',
+                        'surf/lh.inflated.K', 'surf/rh.inflated.K'], []),
+            ('curvstats', ['stats/lh.curv.stats', 'stats/rh.curv.stats'], []),
+            ]
+        _autorecon3_steps = [
+            ('sphere', ['surf/lh.sphere', 'surf/rh.sphere'], []),
+            ('surfreg', ['surf/lh.sphere.reg', 'surf/rh.sphere.reg'], []),
+            ('jacobian_white', ['surf/lh.jacobian_white',
+                                'surf/rh.jacobian_white'], []),
+            ('avgcurv', ['surf/lh.avg_curv', 'surf/rh.avg_curv'], []),
+            ('cortparc', ['label/lh.aparc.annot', 'label/rh.aparc.annot'], []),
+            ('pial', ['surf/lh.pial', 'surf/rh.pial',
+                      'surf/lh.curv.pial', 'surf/rh.curv.pial',
+                      'surf/lh.area.pial', 'surf/rh.area.pial',
+                      'surf/lh.thickness', 'surf/rh.thickness'], []),
+            ('cortribbon', ['mri/lh.ribbon.mgz', 'mri/rh.ribbon.mgz',
+                            'mri/ribbon.mgz'], []),
+            ('parcstats', ['stats/lh.aparc.astats', 'stats/rh.aparc.stats',
+                           'stats/aparc.annot.ctab'], []),
+            ('cortparc2', ['label/lh.aparc.a2009s.annot',
+                           'label/rh.aparc.a2009s.annot'], []),
+            ('parcstats2', ['stats/lh.aparc.a2009s.stats',
+                            'stats/rh.aparc.a2009s.stats',
+                            'stats/aparc.annot.a2009s.ctab'], []),
+            ('cortparc3', ['label/lh.aparc.DKTatlas.annot',
+                           'label/rh.aparc.DKTatlas.annot'], []),
+            ('parcstats3', ['stats/lh.aparc.DKTatlas.stats',
+                            'stats/rh.aparc.DKTatlas.stats',
+                            'stats/aparc.annot.DKTatlas.ctab'], []),
+            ('pctsurfcon', ['surf/lh.w-g.pct.mgh', 'surf/rh.w-g.pct.mgh'], []),
+            ('hyporelabel', ['mri/aseg.presurf.hypos.mgz'], []),
+            ('aparc2aseg', ['mri/aparc+aseg.mgz',
+                            'mri/aparc.a2009s+aseg.mgz',
+                            'mri/aparc.DKTatlas+aseg.mgz'], []),
+            ('apas2aseg', ['mri/aseg.mgz'], ['mri/aparc+aseg.mgz']),
+            ('segstats', ['stats/aseg.stats'], []),
+            ('wmparc', ['mri/wmparc.mgz', 'stats/wmparc.stats'], []),
+            ('balabels', ['BA.ctab', 'BA.thresh.ctab',
+                          'label/lh.entorhinal_exvivo.label',
+                          'label/rh.entorhinal_exvivo.label'], []),
+            ]
+
+    _steps = _autorecon1_steps + _autorecon2_steps + _autorecon3_steps
 
     def _gen_subjects_dir(self):
         return os.getcwd()
@@ -790,24 +888,21 @@ def cmdline(self):
         subjects_dir = self.inputs.subjects_dir
         if not isdefined(subjects_dir):
             subjects_dir = self._gen_subjects_dir()
-        # cmd = cmd.replace(' -all ', ' -make all ')
-        iflogger.info('Overriding recon-all directive')
+
         flags = []
-        directive = 'all'
         for idx, step in enumerate(self._steps):
-            step, outfiles = step
-            if all([os.path.exists(os.path.join(subjects_dir,
-                                                self.inputs.subject_id, f)) for
-                    f in outfiles]):
-                flags.append('-no%s' % step)
-                if idx > 4:
-                    directive = 'autorecon2'
-                elif idx > 23:
-                    directive = 'autorecon3'
-            else:
-                flags.append('-%s' % step)
-        cmd = cmd.replace(' -%s ' % self.inputs.directive, ' -%s ' % directive)
+            step, outfiles, infiles = step
+            flag = '-{}'.format(step)
+            noflag = '-no{}'.format(step)
+            if flag in cmd or noflag in cmd:
+                continue
+
+            subj_dir = os.path.join(subjects_dir, self.inputs.subject_id)
+            if check_depends([os.path.join(subj_dir, f) for f in outfiles],
+                             [os.path.join(subj_dir, f) for f in infiles]):
+                flags.append(noflag)
         cmd += ' ' + ' '.join(flags)
+
         iflogger.info('resume recon-all : %s' % cmd)
         return cmd
 
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 3f7f7462f9..ca5cd66f07 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -447,6 +447,19 @@ def list_to_filename(filelist):
     else:
         return filelist[0]
 
+
+def check_depends(targets, dependencies):
+    """Return true if all targets exist and are newer than all dependencies.
+
+    An OSError will be raised if there are missing dependencies.
+    """
+    tgts = filename_to_list(targets)
+    deps = filename_to_list(dependencies)
+    return all(map(os.path.exists, tgts)) and \
+        min(map(os.path.getmtime, tgts)) > \
+        max(list(map(os.path.getmtime, deps)) + [0])
+
+
 def save_json(filename, data):
     """Save data to a json file
 
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index f0dee52870..644a055f4b 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -5,7 +5,9 @@
 from builtins import open
 
 import os
-from tempfile import mkstemp
+import time
+from tempfile import mkstemp, mkdtemp
+import shutil
 import warnings
 
 import pytest
@@ -15,6 +17,7 @@
                                 hash_rename, check_forhash,
                                 copyfile, copyfiles,
                                 filename_to_list, list_to_filename,
+                                check_depends,
                                 split_filename, get_related_files)
 
 import numpy as np
@@ -271,6 +274,41 @@ def test_list_to_filename(list, expected):
     assert x == expected
 
 
+def test_check_depends():
+    def touch(fname):
+        with open(fname, 'a'):
+            os.utime(fname, None)
+
+    tmpdir = mkdtemp()
+
+    dependencies = [os.path.join(tmpdir, str(i)) for i in range(3)]
+    targets = [os.path.join(tmpdir, str(i)) for i in range(3, 6)]
+
+    # Targets newer than dependencies
+    for dep in dependencies:
+        touch(dep)
+    time.sleep(1)
+    for tgt in targets:
+        touch(tgt)
+    assert check_depends(targets, dependencies)
+
+    # Targets older than newest dependency
+    time.sleep(1)
+    touch(dependencies[0])
+    assert not check_depends(targets, dependencies)
+
+    # Missing dependency
+    os.unlink(dependencies[0])
+    try:
+        check_depends(targets, dependencies)
+    except OSError as e:
+        pass
+    else:
+        assert False, "Should raise OSError on missing dependency"
+
+    shutil.rmtree(tmpdir)   
+
+
 def test_json():
     # Simple roundtrip test of json files, just a sanity check.
     adict = dict(a='one', c='three', b='two')