From 166f20966887fefa7d8be6c26cf1ff1a9ebda41a Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Mon, 4 Apr 2016 14:14:37 -0700
Subject: [PATCH 01/72] fix: sge plugin - no zombies at ucsf

---
 nipype/pipeline/plugins/sge.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py
index 547a3cbbb8..bbe5be9db8 100644
--- a/nipype/pipeline/plugins/sge.py
+++ b/nipype/pipeline/plugins/sge.py
@@ -60,7 +60,7 @@ def is_initializing(self):
         return self._job_queue_state == "initializing"
 
     def is_zombie(self):
-        return self._job_queue_state == "zombie"
+        return self._job_queue_state == "zombie" or self._job_queue_state == "finished"
 
     def is_running(self):
         return self._job_queue_state == "running"

From eea0b9aaf7e94327f8b97702745f318256592b10 Mon Sep 17 00:00:00 2001
From: Alexandre Manhaes Savio <alexsavio@gmail.com>
Date: Thu, 7 Apr 2016 14:05:45 +0200
Subject: [PATCH 02/72] add nipype_crash_search script

---
 bin/nipype_crash_search.py | 76 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100755 bin/nipype_crash_search.py

diff --git a/bin/nipype_crash_search.py b/bin/nipype_crash_search.py
new file mode 100755
index 0000000000..068e5d600a
--- /dev/null
+++ b/bin/nipype_crash_search.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+"""Search for tracebacks inside a folder of nipype crash
+log files that match a given regular expression.
+
+Examples:
+nipype_crash_search -d nipype/wd/log -r '.*subject123.*'
+"""
+import re
+import os.path as op
+from glob import glob
+
+from traits.trait_errors import TraitError
+from nipype.utils.filemanip import loadcrash
+
+
+def load_pklz_traceback(crash_filepath):
+    """ Return the traceback message in the given crash file."""
+    try:
+        data = loadcrash(crash_filepath)
+    except TraitError as te:
+        return str(te)
+    except:
+        raise
+    else:
+        return '\n'.join(data['traceback'])
+
+
+def iter_tracebacks(logdir):
+    """ Return an iterator over each file path and
+    traceback field inside `logdir`.
+    Parameters
+    ----------
+    logdir: str
+        Path to the log folder.
+
+    field: str
+        Field name to be read from the crash file.
+
+    Yields
+    ------
+    path_file: str
+
+    traceback: str
+    """
+    crash_files = sorted(glob(op.join(logdir, '*.pkl*')))
+
+    for cf in crash_files:
+        yield cf, load_pklz_traceback(cf)
+
+
+def display_crash_search(logdir, regex):
+    rex = re.compile(regex, re.IGNORECASE)
+    for file, trace in iter_tracebacks(logdir):
+        if rex.search(trace):
+            print("-" * len(file))
+            print(file)
+            print("-" * len(file))
+            print(trace)
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_crash_search',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument('-l','--logdir', type=str, dest='logdir',
+                        action="store", default=None,
+                        help='The working directory log file.' + defstr)
+    parser.add_argument('-r', '--regex', dest='regex',
+                        default='*',
+                        help='Regular expression to be searched in each traceback.' + defstr)
+
+    args = parser.parse_args()
+
+    display_crash_search(args.logdir, args.regex)

From 98012c81e28472c101df8cf2bd82911c9bdf0c8d Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Mon, 11 Apr 2016 14:49:48 -0700
Subject: [PATCH 03/72] fix: removed list_outputs because it isn't needed

---
 nipype/interfaces/freesurfer/utils.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 1b4b5e3d15..6edb1399e9 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -527,11 +527,6 @@ class ApplyMask(FSCommand):
     input_spec = ApplyMaskInputSpec
     output_spec = ApplyMaskOutputSpec
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
-        return outputs
-
 
 class SurfaceSnapshotsInputSpec(FSTraitedSpec):
 

From 66069cd6a622ed71a5abe2b7c3ec216900a957b9 Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Mon, 11 Apr 2016 15:26:29 -0700
Subject: [PATCH 04/72] doc: make check-before-commit

---
 nipype/workflows/smri/freesurfer/recon.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index c9206812f3..b574314f35 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -82,7 +82,7 @@ def link_masks(subjects_dir, subject_id):
 def create_reconall_workflow(name="ReconAll", plugin_args=None,
                              recoding_file=None):
     """Creates the ReconAll workflow in nipype.
-    
+
     Example
     -------
     >>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
@@ -200,7 +200,7 @@ def checkarg(arg, default):
               'lookup_table',
               'wm_lookup_table',
               'awk_file']
-    
+
     config_node = pe.Node(niu.Function(params,
                                        params,
                                        setconfig),
@@ -509,7 +509,7 @@ def completemethod(datasinked_files, subject_id):
     reconall.connect([(datasink, completion, [('out_file', 'datasinked_files')]),
                       (inputspec, completion, [('subject_id', 'subject_id')]),
                       (completion, postds_outputspec, [('subject_id', 'subject_id')])])
-                                      
+
 
     #### Workflow additions go here
     if recoding_file:

From 9fd5187fcd71f20f42f621473df404541b94f3f7 Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Mon, 11 Apr 2016 16:14:44 -0700
Subject: [PATCH 05/72] doc: make check-before-commit

---
 nipype/workflows/smri/freesurfer/recon.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index c9206812f3..b574314f35 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -82,7 +82,7 @@ def link_masks(subjects_dir, subject_id):
 def create_reconall_workflow(name="ReconAll", plugin_args=None,
                              recoding_file=None):
     """Creates the ReconAll workflow in nipype.
-    
+
     Example
     -------
     >>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
@@ -200,7 +200,7 @@ def checkarg(arg, default):
               'lookup_table',
               'wm_lookup_table',
               'awk_file']
-    
+
     config_node = pe.Node(niu.Function(params,
                                        params,
                                        setconfig),
@@ -509,7 +509,7 @@ def completemethod(datasinked_files, subject_id):
     reconall.connect([(datasink, completion, [('out_file', 'datasinked_files')]),
                       (inputspec, completion, [('subject_id', 'subject_id')]),
                       (completion, postds_outputspec, [('subject_id', 'subject_id')])])
-                                      
+
 
     #### Workflow additions go here
     if recoding_file:

From 34df67cb4d75525f9173cbadf220ef06ff3810d5 Mon Sep 17 00:00:00 2001
From: Chris Gorgolewski <krzysztof.gorgolewski@gmail.com>
Date: Mon, 11 Apr 2016 19:00:59 -0700
Subject: [PATCH 06/72] Added Gitter Sidecar

---
 doc/_templates/layout.html | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/_templates/layout.html b/doc/_templates/layout.html
index 8a3b08697e..a8de8d176b 100644
--- a/doc/_templates/layout.html
+++ b/doc/_templates/layout.html
@@ -14,6 +14,12 @@
   ga('create', 'UA-339450-7', 'nipy.org/nipype');
   ga('send', 'pageview');
 </script>
+<script>
+  ((window.gitter = {}).chat = {}).options = {
+    room: 'nipy/nipype'
+  };
+</script>
+<script src="https://sidecar.gitter.im/dist/sidecar.v1.js" async defer></script>
 {% endblock %}
 
 {% block header %}

From dba3270e98d12ba65b4030b9315d7ca63ccb7d79 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <effigies@bu.edu>
Date: Tue, 12 Apr 2016 13:15:51 -0400
Subject: [PATCH 07/72] REF: Simplify checkT1s

* Use nibabel instead of SimpleITK to determine image shape
* Do not convert .mgz to .nii
* Simplify error checking and origvol_names with comprehensions
* PEP8 cleanup in/around checkT1s
---
 .../workflows/smri/freesurfer/autorecon1.py   | 57 +++++++------------
 1 file changed, 20 insertions(+), 37 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index bc4fb8bff2..b77b65465c 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -6,53 +6,36 @@
 from nipype.interfaces.freesurfer import *
 from .utils import copy_file, copy_files
 
+
 def checkT1s(T1_files, cw256=False):
     """Verifying size of inputs and setting workflow parameters"""
-    import SimpleITK as sitk
-    import os
     import sys
-    # check that the files are in a list
-    if not type(T1_files) == list:
-        T1_files = [T1_files]
+    import nibabel as nib
+    from nipype.utils.filemanip import filename_to_list
+
+    T1_files = filename_to_list(T1_files)
     if len(T1_files) == 0:
         print("ERROR: No T1's Given")
         sys.exit(-1)
-    for i, t1 in enumerate(T1_files):
-        if t1.endswith(".mgz"):
-            # convert input fs files to NIFTI
-            convert = MRIConvert()
-            convert.inputs.in_file = t1
-            convert.inputs.out_file = os.path.abspath(os.path.basename(t1).replace('.mgz', '.nii.gz'))
-            convert.run()
-            T1_files[i] = convert.inputs.out_file
-    size = None
-    origvol_names = list()
-    for i, t1 in enumerate(T1_files):
-        # assign an input number
-        file_num = str(i + 1)
-        while len(file_num) < 3:
-            file_num = '0' + file_num
-        origvol_names.append("{0}.mgz".format(file_num))
-        # check the size of the image
-        img = sitk.ReadImage(t1)
-        if not size:
-            size = img.GetSize()
-        elif size != img.GetSize():
-            print("ERROR: T1s not the same size. Cannot process {0} {1} together".format(T1_files[0],
-                                                                                         otherFilename))
+
+    shape = nib.load(T1_files[0]).shape
+    for t1 in T1_files[1:]:
+        if nib.load(t1).shape != shape:
+            print("ERROR: T1s not the same size. Cannot process {0} and {1} "
+                  "together".format(T1_files[0], t1))
             sys.exit(-1)
+
+    origvol_names = ["{0:03d}.mgz".format(i + 1) for i in range(len(T1_files))]
+
     # check if cw256 is set to crop the images if size is larger than 256
-    if not cw256:
-        for dim in size:
-            if dim > 256:
-                print("Setting MRI Convert to crop images to 256 FOV")
-                cw256 = True
-    if len(T1_files) > 1:
-        resample_type = 'cubic'
-    else:
-        resample_type = 'interpolate'
+    if not cw256 and any(dim > 256 for dim in shape):
+        print("Setting MRI Convert to crop images to 256 FOV")
+        cw256 = True
+
+    resample_type = 'cubic' if len(T1_files) > 1 else 'interpolate'
     return T1_files, cw256, resample_type, origvol_names
 
+
 def create_AutoRecon1(name="AutoRecon1", longitudinal=False, field_strength='1.5T',
                       custom_atlas=None, plugin_args=None):
     """Creates the AutoRecon1 workflow in nipype.

From 0fd5842183233687f0dc62cf4fd66d43698cea13 Mon Sep 17 00:00:00 2001
From: akeshavan <keshavan@berkeley.edu>
Date: Tue, 12 Apr 2016 12:42:53 -0700
Subject: [PATCH 08/72] fix: segstats avgwf_txt_file can be a bool without
 error

---
 nipype/interfaces/freesurfer/model.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
index 607586d6f6..2980f147d8 100644
--- a/nipype/interfaces/freesurfer/model.py
+++ b/nipype/interfaces/freesurfer/model.py
@@ -752,8 +752,9 @@ def _list_outputs(self):
 
     def _format_arg(self, name, spec, value):
         if name in ('summary_file', 'avgwf_txt_file'):
-            if not os.path.isabs(value):
-                value = os.path.join('.', value)
+            if not isinstance(value, bool):
+                if not os.path.isabs(value):
+                    value = os.path.join('.', value)
         if name in ['avgwf_txt_file', 'avgwf_file', 'sf_avg_file']:
             if isinstance(value, bool):
                 fname = self._list_outputs()[name]

From 2ce38f4d5e92927bc4ed687f59fc537510b303ab Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:21:04 -0500
Subject: [PATCH 09/72] FIX: Fixes a few flags in for FreeSurfer 5.3

---
 .../workflows/smri/freesurfer/autorecon1.py   | 25 ++++++----------
 .../workflows/smri/freesurfer/autorecon3.py   |  4 +--
 nipype/workflows/smri/freesurfer/ba_maps.py   | 13 +++++++--
 nipype/workflows/smri/freesurfer/recon.py     | 29 +++++++++++++++++--
 4 files changed, 48 insertions(+), 23 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index b77b65465c..dca938c4c2 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -35,9 +35,8 @@ def checkT1s(T1_files, cw256=False):
     resample_type = 'cubic' if len(T1_files) > 1 else 'interpolate'
     return T1_files, cw256, resample_type, origvol_names
 
-
-def create_AutoRecon1(name="AutoRecon1", longitudinal=False, field_strength='1.5T',
-                      custom_atlas=None, plugin_args=None):
+def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
+                      custom_atlas=None, plugin_args=None, shrink=2):
     """Creates the AutoRecon1 workflow in nipype.
 
     Inputs::
@@ -238,19 +237,13 @@ def createTemplate(in_files, out_file):
     bias_correction = pe.Node(MNIBiasCorrection(), name="Bias_correction")
     bias_correction.inputs.iterations = 1
     bias_correction.inputs.protocol_iterations = 1000
-    if field_strength == '3T':
-        # 3T params from Zheng, Chee, Zagorodnov 2009 NeuroImage paper
-        # "Improvement of brain segmentation accuracy by optimizing
-        # non-uniformity correction using N3"
-        # namely specifying iterations, proto-iters and distance:
-        bias_correction.inputs.distance = 50
-    else:
-        # 1.5T default
-        bias_correction.inputs.distance = 200
-    # per c.larsen, decrease convergence threshold (default is 0.001)
-    bias_correction.inputs.stop = 0.0001
-    # per c.larsen, decrease shrink parameter: finer sampling (default is 4)
-    bias_correction.inputs.shrink =  2
+    bias_correction.inputs.distance = distance
+    if stop:
+        # per c.larsen, decrease convergence threshold (default is 0.001)
+        bias_correction.inputs.stop = stop
+    if shrink:
+        # per c.larsen, decrease shrink parameter: finer sampling (default is 4)
+        bias_correction.inputs.shrink =  shrink
     # add the mask, as per c.larsen, bias-field correction is known to work
     # much better when the brain area is properly masked, in this case by
     # brainmask.mgz.
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index ffc0eec7b9..bf383231f5 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -8,7 +8,7 @@
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
-                      th3=True):
+                      th3=True, exvivo=True):
 
     # AutoRecon3
     # Workflow
@@ -705,7 +705,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     ])
 
     # add brodman area maps to the workflow
-    ba_WF, ba_outputs = create_ba_maps_wf(th3=th3)
+    ba_WF, ba_outputs = create_ba_maps_wf(th3=th3, exvivo=exvivo)
 
     ar3_wf.connect([(ar3_lh_wf1, ba_WF, [('outputspec.sphere_reg', 'inputspec.lh_sphere_reg'),
                                          ('outputspec.thickness_pial', 'inputspec.lh_thickness'),
diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 337e1f40cb..8e39726ece 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -6,7 +6,7 @@
 from nipype.interfaces.io import DataGrabber
 from nipype.interfaces.utility import Merge
 
-def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True):
+def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True):
     # Brodmann Area Maps (BA Maps) and Hinds V1 Atlas
     inputs = ['lh_sphere_reg',
               'rh_sphere_reg',
@@ -64,13 +64,20 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True):
             out_files = list()
             if threshold:
                 for label in labels:
-                    out_file = '{0}.{1}_exvivo.thresh.label'.format(hemisphere, label)
+                    if exvivo:
+                        out_file = '{0}.{1}_exvivo.thresh.label'.format(hemisphere, label)
+                    else:
+                        out_file = '{0}.{1}.thresh.label'.format(hemisphere, label)
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
                 node_name = 'BA_Maps_' + hemisphere + '_Tresh'
             else:
                 for label in labels:
-                    out_file = '{0}.{1}_exvivo.label'.format(hemisphere, label)
+                    if exvivo:
+                        out_file = '{0}.{1}_exvivo.label'.format(hemisphere, label)
+                    else:
+                        out_file = '{0}.{1}.label'.format(hemisphere, label)
+                        
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
                 node_name = 'BA_Maps_' + hemisphere
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index b574314f35..376f0b695e 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -4,7 +4,7 @@
 from .autorecon1 import create_AutoRecon1
 from .autorecon2 import create_AutoRecon2
 from .autorecon3 import create_AutoRecon3
-from ....interfaces.freesurfer import AddXFormToHeader
+from ....interfaces.freesurfer import AddXFormToHeader, Info
 from ....interfaces.io import DataSink
 from .utils import getdefaultconfig
 
@@ -135,6 +135,30 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
                         run_without_submitting=True,
                         name='inputspec')
 
+    # check freesurfer version and set parameters
+    fs_version_full = Info.version()
+    elif 'v6.0' in fs_version_full or 'dev' in fs_version_full:
+        # assuming that dev is 6.0
+        fs_version = '6.0'
+        th3 = True
+        shrink = 2
+        distance = 200 # 3T should be 50
+        exvivo = True
+    else:
+        # 5.3 is default
+        if 'v5.3' in fs_version_full:
+            fs_version = '5.3'
+        else:
+            fs_vesion = fs_version_full.split('-')[-1]
+            print("Warning: Workflow may not work properly if FREESURFER_HOME " +
+                  "environmental variable is not set or if you are using an older " +
+                  "version of FreeSurfer")
+        th3 = False
+        shrink = None
+        exvivo = False
+        distance = 50
+        stop = None
+    
     def setconfig(reg_template=None,
                   reg_template_withskull=None,
                   lh_atlas=None,
@@ -232,7 +256,8 @@ def checkarg(arg, default):
                                         ('outputspec.talairach', 'inputspec.transform'),
                                         ('outputspec.orig', 'inputspec.orig')])])
     # create AutoRecon3
-    ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=True)
+    ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=th3,
+                                            exvivo=exvivo)
     # connect inputs for AutoRecon3
     reconall.connect([(config_node, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
                                              ('rh_atlas', 'inputspec.rh_atlas'),

From 7a43049a8207ee259019bb0798aea92f14ae3416 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:25:28 -0500
Subject: [PATCH 10/72] ENH: Print FS version.

---
 nipype/workflows/smri/freesurfer/recon.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 376f0b695e..efd2583f16 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -139,7 +139,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
     fs_version_full = Info.version()
     elif 'v6.0' in fs_version_full or 'dev' in fs_version_full:
         # assuming that dev is 6.0
-        fs_version = '6.0'
+        fs_version = 'v6.0'
         th3 = True
         shrink = 2
         distance = 200 # 3T should be 50
@@ -147,7 +147,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
     else:
         # 5.3 is default
         if 'v5.3' in fs_version_full:
-            fs_version = '5.3'
+            fs_version = 'v5.3'
         else:
             fs_vesion = fs_version_full.split('-')[-1]
             print("Warning: Workflow may not work properly if FREESURFER_HOME " +
@@ -158,7 +158,9 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         exvivo = False
         distance = 50
         stop = None
-    
+
+    print("FreeSurfer Version: {0}".format(fs_version))
+        
     def setconfig(reg_template=None,
                   reg_template_withskull=None,
                   lh_atlas=None,

From ee7ab69fbba33796c34cfade670d5d014268fbc5 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:27:30 -0500
Subject: [PATCH 11/72] FIX: Fixes elif syntax error.

---
 nipype/workflows/smri/freesurfer/recon.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index efd2583f16..4646f90334 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -137,7 +137,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
 
     # check freesurfer version and set parameters
     fs_version_full = Info.version()
-    elif 'v6.0' in fs_version_full or 'dev' in fs_version_full:
+    if 'v6.0' in fs_version_full or 'dev' in fs_version_full:
         # assuming that dev is 6.0
         fs_version = 'v6.0'
         th3 = True

From dc8fec34bb811df103f44c900f01dff5c53f6b91 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:33:14 -0500
Subject: [PATCH 12/72] FIX: Adds stop and shrink to autorecon1.

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 2 +-
 nipype/workflows/smri/freesurfer/recon.py      | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index dca938c4c2..db26ea77d4 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -36,7 +36,7 @@ def checkT1s(T1_files, cw256=False):
     return T1_files, cw256, resample_type, origvol_names
 
 def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
-                      custom_atlas=None, plugin_args=None, shrink=2):
+                      custom_atlas=None, plugin_args=None, shrink=2, stop=0.0001):
     """Creates the AutoRecon1 workflow in nipype.
 
     Inputs::
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 4646f90334..2f6967e15b 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -143,6 +143,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         th3 = True
         shrink = 2
         distance = 200 # 3T should be 50
+        stop = 0.0001
         exvivo = True
     else:
         # 5.3 is default
@@ -155,9 +156,9 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
                   "version of FreeSurfer")
         th3 = False
         shrink = None
-        exvivo = False
         distance = 50
         stop = None
+        exvivo = False
 
     print("FreeSurfer Version: {0}".format(fs_version))
         
@@ -236,7 +237,8 @@ def checkarg(arg, default):
         reconall.connect(inputspec, param, config_node, param)
 
     # create AutoRecon1
-    ar1_wf, ar1_outputs = create_AutoRecon1(plugin_args=plugin_args)
+    ar1_wf, ar1_outputs = create_AutoRecon1(plugin_args=plugin_args, stop=stop,
+                                            distance=distance, shrink=shrink)
     # connect inputs for AutoRecon1
     reconall.connect([(inputspec, ar1_wf, [('T1_files', 'inputspec.T1_files'),
                                            ('T2_file', 'inputspec.T2_file'),

From c79f559dd9c78b4a7d3b1f8bdfbe2121626352a8 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:46:13 -0500
Subject: [PATCH 13/72] FIX: Removes entorhinal BA maps for 5.3.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 3 ++-
 nipype/workflows/smri/freesurfer/ba_maps.py    | 7 +++++--
 nipype/workflows/smri/freesurfer/recon.py      | 4 +++-
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index bf383231f5..7d64095ae2 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -705,7 +705,8 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     ])
 
     # add brodman area maps to the workflow
-    ba_WF, ba_outputs = create_ba_maps_wf(th3=th3, exvivo=exvivo)
+    ba_WF, ba_outputs = create_ba_maps_wf(th3=th3, exvivo=exvivo,
+                                          entorhinal=entorhinal)
 
     ar3_wf.connect([(ar3_lh_wf1, ba_WF, [('outputspec.sphere_reg', 'inputspec.lh_sphere_reg'),
                                          ('outputspec.thickness_pial', 'inputspec.lh_thickness'),
diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 8e39726ece..c586bbb0ee 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -6,7 +6,8 @@
 from nipype.interfaces.io import DataGrabber
 from nipype.interfaces.utility import Merge
 
-def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True):
+def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
+                      entorhinal=True):
     # Brodmann Area Maps (BA Maps) and Hinds V1 Atlas
     inputs = ['lh_sphere_reg',
               'rh_sphere_reg',
@@ -55,7 +56,9 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True):
                          name="outputspec")
 
     labels = ["BA1", "BA2", "BA3a", "BA3b", "BA4a", "BA4p", "BA6",
-              "BA44", "BA45", "V1", "V2", "MT", "entorhinal", "perirhinal"]
+              "BA44", "BA45", "V1", "V2", "MT", "perirhinal"]
+    if entorhinal:
+        labels.append('entorhinal')
     for hemisphere in ['lh', 'rh']:
         for threshold in [True, False]:
             field_template = dict(sphere_reg='surf/{0}.sphere.reg'.format(hemisphere),
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 2f6967e15b..a7791b49e8 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -145,6 +145,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         distance = 200 # 3T should be 50
         stop = 0.0001
         exvivo = True
+        entorhinal = True
     else:
         # 5.3 is default
         if 'v5.3' in fs_version_full:
@@ -159,6 +160,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         distance = 50
         stop = None
         exvivo = False
+        entorhinal = False
 
     print("FreeSurfer Version: {0}".format(fs_version))
         
@@ -261,7 +263,7 @@ def checkarg(arg, default):
                                         ('outputspec.orig', 'inputspec.orig')])])
     # create AutoRecon3
     ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=th3,
-                                            exvivo=exvivo)
+                                            exvivo=exvivo, entorhinal=entorhinal)
     # connect inputs for AutoRecon3
     reconall.connect([(config_node, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
                                              ('rh_atlas', 'inputspec.rh_atlas'),

From bfa3c2995e4b7192886000925927710cd968c8f0 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 09:51:27 -0500
Subject: [PATCH 14/72] FIX: Adds entorhinal to autorecon3

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 7d64095ae2..d0dc354677 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -8,7 +8,7 @@
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
-                      th3=True, exvivo=True):
+                      th3=True, exvivo=True, entorhinal=True):
 
     # AutoRecon3
     # Workflow

From 291bafd9e6696c0be5adbf09e596f6a1f15a1a03 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 10:04:04 -0500
Subject: [PATCH 15/72] FIX: Removes thresh.perirhinal from 5.3

---
 nipype/workflows/smri/freesurfer/ba_maps.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index c586bbb0ee..6602fdeeb5 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -67,6 +67,9 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
             out_files = list()
             if threshold:
                 for label in labels:
+                    if label == 'perirhinal' and entorhinal:
+                        # versions < 6.0 do not use thresh.perirhinal
+                        continue
                     if exvivo:
                         out_file = '{0}.{1}_exvivo.thresh.label'.format(hemisphere, label)
                     else:

From 4bd496236f553ec0b80da414247db941b2a0f44f Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 10:13:28 -0500
Subject: [PATCH 16/72] FIX: Allows for changing of RB atlas

---
 nipype/workflows/smri/freesurfer/recon.py | 7 +++++--
 nipype/workflows/smri/freesurfer/utils.py | 6 +++---
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index a7791b49e8..15eb7b7930 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -146,6 +146,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         stop = 0.0001
         exvivo = True
         entorhinal = True
+        rb_date = "2014-08-21"
     else:
         # 5.3 is default
         if 'v5.3' in fs_version_full:
@@ -161,6 +162,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         stop = None
         exvivo = False
         entorhinal = False
+        rb_date = "2008-03-26"
 
     print("FreeSurfer Version: {0}".format(fs_version))
         
@@ -179,7 +181,8 @@ def setconfig(reg_template=None,
                   color_table=None,
                   lookup_table=None,
                   wm_lookup_table=None,
-                  awk_file=None):
+                  awk_file=None,
+                  rb_date=rb_date):
         """Set optional configurations to the default"""
         from nipype.workflows.smri.freesurfer.utils import getdefaultconfig
         def checkarg(arg, default):
@@ -188,7 +191,7 @@ def checkarg(arg, default):
                 return arg
             else:
                 return default
-        defaultconfig = getdefaultconfig(exitonfail=True)
+        defaultconfig = getdefaultconfig(exitonfail=True, rb_date=rb_date)
         # set the default template and classifier files
         reg_template = checkarg(reg_template, defaultconfig['registration_template'])
         reg_template_withskull = checkarg(reg_template_withskull,
diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 7ce98a4642..69eb22911e 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -420,7 +420,7 @@ def mkdir_p(path):
         else:
             raise
 
-def getdefaultconfig(exitonfail=False):
+def getdefaultconfig(exitonfail=False, rb_date="2014-08-21"):
     config = { 'custom_atlas' : None,
                'cw256' : False,
                'field_strength' : '1.5T',
@@ -440,9 +440,9 @@ def getdefaultconfig(exitonfail=False):
     config['awk_file'] = os.path.join(config['fs_home'], 'bin',
                                       'extract_talairach_avi_QA.awk')
     config['registration_template'] = os.path.join(config['fs_home'], 'average',
-                                                   'RB_all_2014-08-21.gca')
+                                                   'RB_all_{0}.gca'.format(rb_date))
     config['registration_template_withskull'] = os.path.join(config['fs_home'], 'average',
-                                                             'RB_all_withskull_2014-08-21.gca')
+                                                             'RB_all_withskull_{0}.gca'.format(rb_date))
     for hemi in ('lh', 'rh'):
         config['{0}_atlas'.format(hemi)] = os.path.join(
             config['fs_home'], 'average',

From c8ddf6dfc4f34364889fbd0c4bc6c7726a24da32 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 10:26:37 -0500
Subject: [PATCH 17/72] FIX: Fixes input to config for rb_date

---
 nipype/workflows/smri/freesurfer/recon.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 15eb7b7930..fb5b1d3d22 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -182,7 +182,7 @@ def setconfig(reg_template=None,
                   lookup_table=None,
                   wm_lookup_table=None,
                   awk_file=None,
-                  rb_date=rb_date):
+                  rb_date=None):
         """Set optional configurations to the default"""
         from nipype.workflows.smri.freesurfer.utils import getdefaultconfig
         def checkarg(arg, default):
@@ -232,12 +232,14 @@ def checkarg(arg, default):
               'lookup_table',
               'wm_lookup_table',
               'awk_file']
-
-    config_node = pe.Node(niu.Function(params,
+    
+    config_node = pe.Node(niu.Function(params.append('rb_date'),
                                        params,
                                        setconfig),
                           name="config")
 
+    config_node.inputs.rb_date = rb_date
+    
     for param in params:
         reconall.connect(inputspec, param, config_node, param)
 

From e81d637243686c16685d2d38abca86fb9c053081 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 12:36:59 -0500
Subject: [PATCH 18/72] FIX: config function.

---
 nipype/workflows/smri/freesurfer/recon.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index fb5b1d3d22..33db7bd44c 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -233,7 +233,7 @@ def checkarg(arg, default):
               'wm_lookup_table',
               'awk_file']
     
-    config_node = pe.Node(niu.Function(params.append('rb_date'),
+    config_node = pe.Node(niu.Function(params + ['rb_date'],
                                        params,
                                        setconfig),
                           name="config")

From 97e1021c8a66ef5ced475ea1712b384de5194b55 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 15:01:32 -0500
Subject: [PATCH 19/72] FIX: Switches around the intensity normalization for
 5.3

---
 .../workflows/smri/freesurfer/autorecon1.py   | 51 +++++++---
 .../workflows/smri/freesurfer/autorecon2.py   | 95 +++++++++++--------
 nipype/workflows/smri/freesurfer/ba_maps.py   |  2 +-
 nipype/workflows/smri/freesurfer/recon.py     |  7 +-
 4 files changed, 101 insertions(+), 54 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index db26ea77d4..a258bc5dd4 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -36,7 +36,8 @@ def checkT1s(T1_files, cw256=False):
     return T1_files, cw256, resample_type, origvol_names
 
 def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
-                      custom_atlas=None, plugin_args=None, shrink=2, stop=0.0001):
+                      custom_atlas=None, plugin_args=None, shrink=2, stop=0.0001,
+                      fsvernum=5.3):
     """Creates the AutoRecon1 workflow in nipype.
 
     Inputs::
@@ -239,14 +240,9 @@ def createTemplate(in_files, out_file):
     bias_correction.inputs.protocol_iterations = 1000
     bias_correction.inputs.distance = distance
     if stop:
-        # per c.larsen, decrease convergence threshold (default is 0.001)
         bias_correction.inputs.stop = stop
     if shrink:
-        # per c.larsen, decrease shrink parameter: finer sampling (default is 4)
         bias_correction.inputs.shrink =  shrink
-    # add the mask, as per c.larsen, bias-field correction is known to work
-    # much better when the brain area is properly masked, in this case by
-    # brainmask.mgz.
     bias_correction.inputs.no_rescale = True
     bias_correction.inputs.out_file = 'orig_nu.mgz'
 
@@ -340,6 +336,28 @@ def awkfile(in_file, log_file):
         tal_qc = pe.Node(TalairachQC(), name="Detect_Aligment_Failures")
         ar1_wf.connect([(awk_logfile, tal_qc, [('log_file', 'log_file')])])
 
+
+    if fsvernum < 6:
+        # intensity correction is performed before normalization
+        intensity_correction = pe.Node(
+            MNIBiasCorrection(), name="Intensity_Correction")
+        intensity_correction.inputs.out_file = 'nu.mgz'
+        intensity_correction.inputs.iterations = 2
+        ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
+                                                           ('brainmask', 'mask'),
+                                                           ('transform', 'transform')])])
+        
+
+        add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
+        add_to_header_nu.inputs.copy_name = True
+        add_to_header_nu.inputs.out_file = 'nu.mgz'
+        ar2_wf.connect([(intensity_correction, add_to_header_nu, [('out_file', 'in_file'),
+                                                              ]),
+                        (copy_transform, add_to_header_nu,
+                         [('out_file', 'transform')])
+                    ])
+
+        
     # Intensity Normalization
     # Performs intensity normalization of the orig volume and places the result in mri/T1.mgz.
     # Attempts to correct for fluctuations in intensity that would otherwise make intensity-based
@@ -349,10 +367,13 @@ def awkfile(in_file, log_file):
     mri_normalize = pe.Node(Normalize(), name="Normalize_T1")
     mri_normalize.inputs.gradient = 1
     mri_normalize.inputs.out_file = 'T1.mgz'
-    ar1_wf.connect([(add_xform_to_orig_nu, mri_normalize, [('out_file', 'in_file')]),
-                    (copy_transform, mri_normalize,
-                     [('out_file', 'transform')]),
-                    ])
+
+    if fsvernum < 6:
+        ar1_wf.connect([(add_to_header_nu, mri_normalize, [('out_file', 'in_file')])])        
+    else:
+        ar1_wf.connect([(add_xform_to_orig_nu, mri_normalize, [('out_file', 'in_file')])])
+
+    ar1_wf.connect([(copy_transform, mri_normalize, [('out_file', 'transform')])])
 
     # Skull Strip
     """
@@ -422,8 +443,14 @@ def awkfile(in_file, log_file):
                'brainmask_auto',
                'brainmask',
                'braintemplate']
-    outputspec = pe.Node(IdentityInterface(fields=outputs),
-                         name="outputspec")
+
+    if fsvernum < 6:
+        outputspec = pe.Node(IdentityInterface(fields=outputs + 'nu'),
+                             name="outputspec")
+        ar1_wf.connect([(add_to_header_nu, outputspec, [('out_file', 'nu')])])
+    else:
+        outputspec = pe.Node(IdentityInterface(fields=outputs),
+                             name="outputspec")
 
     ar1_wf.connect([(T1_image_preparation, outputspec, [('out_file', 'origvols')]),
                     (T2_convert, outputspec, [('out_file', 't2_raw')]),
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 2fd85bce13..955dbb93f2 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -11,12 +11,13 @@ def copy_ltas(in_file, subjects_dir, subject_id, long_template):
     return out_file
 
 def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
-                      field_strength="1.5T", plugin_args=None):
+                      plugin_args=None, fsvernum=5.3):
     # AutoRecon2
     # Workflow
     ar2_wf = pe.Workflow(name=name)
 
     inputspec = pe.Node(IdentityInterface(fields=['orig',
+                                                  'nu', # version < 6
                                                   'brainmask',
                                                   'transform',
                                                   'subject_id',
@@ -47,40 +48,39 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         inputspec.inputs.timepoints = config['timepoints']
 
 
-    # NU Intensity Correction
-    """
-    Non-parametric Non-uniform intensity Normalization (N3), corrects for
-    intensity non-uniformity in MR data, making relatively few assumptions about
-    the data. This runs the MINC tool 'nu_correct'.
-    """
-    intensity_correction = pe.Node(
-        MNIBiasCorrection(), name="Intensity_Correction")
-    intensity_correction.inputs.iterations = 1
-    intensity_correction.inputs.protocol_iterations = 1000
-    intensity_correction.inputs.stop = 0.0001
-    intensity_correction.inputs.shrink = 2
-    if field_strength == '3T':
-        intensity_correction.inputs.distance = 50
-    else:
-        # default for 1.5T scans
-        intensity_correction.inputs.distance = 200
-
-    intensity_correction.inputs.out_file = 'nu.mgz'
-    ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
-                                                        ('brainmask', 'mask'),
-                                                        ('transform', 'transform')
-                                                        ])
-                    ])
-
-    add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
-    add_to_header_nu.inputs.copy_name = True
-    add_to_header_nu.inputs.out_file = 'nu.mgz'
-    ar2_wf.connect([(intensity_correction, add_to_header_nu, [('out_file', 'in_file'),
+    if fsvernum >= 6:
+        # NU Intensity Correction
+        """
+        Non-parametric Non-uniform intensity Normalization (N3), corrects for
+        intensity non-uniformity in MR data, making relatively few assumptions about
+        the data. This runs the MINC tool 'nu_correct'.
+        """
+        intensity_correction = pe.Node(
+            MNIBiasCorrection(), name="Intensity_Correction")
+        intensity_correction.inputs.out_file = 'nu.mgz'
+        ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
+                                                           ('brainmask', 'mask'),
+                                                           ('transform', 'transform')])])
+        
+        # intensity correction parameters are more specific in 6+
+        intensity_correction.inputs.iterations = 1
+        intensity_correction.inputs.protocol_iterations = 1000
+        if stop:
+            intensity_correction.inputs.stop = stop
+        if shrink:
+            intensity_correction.inputs.shrink =  shrink
+        intensity_correction.inputs.distance = distance
+        
+        add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
+        add_to_header_nu.inputs.copy_name = True
+        add_to_header_nu.inputs.out_file = 'nu.mgz'
+        ar2_wf.connect([(intensity_correction, add_to_header_nu, [('out_file', 'in_file'),
                                                               ]),
-                    (inputspec, add_to_header_nu,
-                     [('transform', 'transform')])
+                        (inputspec, add_to_header_nu,
+                         [('transform', 'transform')])
                     ])
 
+
     # EM Registration
     """
     Computes the transform to align the mri/nu.mgz volume to the default GCA
@@ -103,8 +103,12 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
             align_transform.plugin_args = plugin_args
         ar2_wf.connect([(inputspec, align_transform, [('brainmask', 'mask'),
                                                       ('reg_template', 'template'),
-                                                      ('num_threads', 'num_threads')]),
-                        (add_to_header_nu, align_transform, [('out_file', 'in_file')])])
+                                                      ('num_threads', 'num_threads')])])
+        if fsvernum >= 6:
+            ar2_wf.connect([(add_to_header_nu, align_transform, [('out_file', 'in_file')])])
+        else:
+            ar2_wf.connect([(inputspec, align_transform, [('nu', 'in_file')])])
+            
 
     # CA Normalize
     """
@@ -128,8 +132,12 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
 
     ar2_wf.connect([(align_transform, ca_normalize, [('out_file', 'transform')]),
                     (inputspec, ca_normalize, [('brainmask', 'mask'),
-                                               ('reg_template', 'atlas')]),
-                    (add_to_header_nu, ca_normalize, [('out_file', 'in_file')])])
+                                               ('reg_template', 'atlas')])])
+    if fsvernum >= 6:
+        ar2_wf.connect([(add_to_header_nu, ca_normalize, [('out_file', 'in_file')])])
+    else:
+        ar2_wf.connect([(inputspec, ca_normalize, [('nu', 'in_file')])])
+
 
     # CA Register
     # Computes a nonlinear transform to align with GCA atlas.
@@ -159,8 +167,11 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
     remove_neck.inputs.radius = 25
     remove_neck.inputs.out_file = 'nu_noneck.mgz'
     ar2_wf.connect([(ca_register, remove_neck, [('out_file', 'transform')]),
-                    (add_to_header_nu, remove_neck, [('out_file', 'in_file')]),
                     (inputspec, remove_neck, [('reg_template', 'template')])])
+    if fsvernum >= 6:
+        ar2_wf.connect([(add_to_header_nu, remove_neck, [('out_file', 'in_file')])])
+    else:
+        ar2_wf.connect([(inputspec, remove_neck, [('nu', 'in_file')])])
 
     # SkullLTA (EM Registration, with Skull)
     # Computes transform to align volume mri/nu_noneck.mgz with GCA volume
@@ -680,8 +691,14 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
     outputspec = pe.Node(IdentityInterface(fields=outputs),
                          name="outputspec")
 
-    ar2_wf.connect([(add_to_header_nu, outputspec, [('out_file', 'nu')]),
-                    (align_transform, outputspec, [('out_file', 'tal_lta')]),
+    if fsvernum >= 6:
+        ar2_wf.connect([(add_to_header_nu, outputspec, [('out_file', 'nu')])])
+    else:
+        # add to outputspec to perserve datasinking
+        ar2_wf.connect([(inputspec, outputspec, [('nu', 'nu')])])
+
+    
+    ar2_wf.connect([(align_transform, outputspec, [('out_file', 'tal_lta')]),
                     (ca_normalize, outputspec, [('out_file', 'norm')]),
                     (ca_normalize, outputspec, [('control_points', 'ctrl_pts')]),
                     (ca_register, outputspec, [('out_file', 'tal_m3z')]),
diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 6602fdeeb5..a8054e9669 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -67,7 +67,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
             out_files = list()
             if threshold:
                 for label in labels:
-                    if label == 'perirhinal' and entorhinal:
+                    if label == 'perirhinal' and not entorhinal:
                         # versions < 6.0 do not use thresh.perirhinal
                         continue
                     if exvivo:
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 33db7bd44c..e44091cdd9 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -139,6 +139,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
     fs_version_full = Info.version()
     if 'v6.0' in fs_version_full or 'dev' in fs_version_full:
         # assuming that dev is 6.0
+        fsvernum = 6.0
         fs_version = 'v6.0'
         th3 = True
         shrink = 2
@@ -149,6 +150,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         rb_date = "2014-08-21"
     else:
         # 5.3 is default
+        fsvernum = 5.3
         if 'v5.3' in fs_version_full:
             fs_version = 'v5.3'
         else:
@@ -245,7 +247,8 @@ def checkarg(arg, default):
 
     # create AutoRecon1
     ar1_wf, ar1_outputs = create_AutoRecon1(plugin_args=plugin_args, stop=stop,
-                                            distance=distance, shrink=shrink)
+                                            distance=distance, shrink=shrink,
+                                            fsvernum=fsvernum)
     # connect inputs for AutoRecon1
     reconall.connect([(inputspec, ar1_wf, [('T1_files', 'inputspec.T1_files'),
                                            ('T2_file', 'inputspec.T2_file'),
@@ -257,7 +260,7 @@ def checkarg(arg, default):
                                              ('awk_file', 'inputspec.awk_file')])])
 
     # create AutoRecon2
-    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args)
+    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum)
     # connect inputs for AutoRecon2
     reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads')]),
                       (config_node, ar2_wf, [('reg_template_withskull',

From c1f8aed231da7fdeba6770fb2404c4b94b660628 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 15:06:39 -0500
Subject: [PATCH 20/72] FIX: fixes connections ar1

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index a258bc5dd4..975382e761 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -343,15 +343,14 @@ def awkfile(in_file, log_file):
             MNIBiasCorrection(), name="Intensity_Correction")
         intensity_correction.inputs.out_file = 'nu.mgz'
         intensity_correction.inputs.iterations = 2
-        ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
-                                                           ('brainmask', 'mask'),
-                                                           ('transform', 'transform')])])
+        ar1_wf.connect([(add_xform_to_orig, intensity_correction, [('out_file', 'in_file')]),
+                        (copy_transform, intensity_correction, [('transform', 'transform')])])
         
 
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
         add_to_header_nu.inputs.copy_name = True
         add_to_header_nu.inputs.out_file = 'nu.mgz'
-        ar2_wf.connect([(intensity_correction, add_to_header_nu, [('out_file', 'in_file'),
+        ar1_wf.connect([(intensity_correction, add_to_header_nu, [('out_file', 'in_file'),
                                                               ]),
                         (copy_transform, add_to_header_nu,
                          [('out_file', 'transform')])

From 4d160087ad6b7930aa829f72aeda7e1ec6a2155c Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 15:08:02 -0500
Subject: [PATCH 21/72] FIX: corrects the output for copy_transform

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index 975382e761..1979a5c235 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -344,7 +344,7 @@ def awkfile(in_file, log_file):
         intensity_correction.inputs.out_file = 'nu.mgz'
         intensity_correction.inputs.iterations = 2
         ar1_wf.connect([(add_xform_to_orig, intensity_correction, [('out_file', 'in_file')]),
-                        (copy_transform, intensity_correction, [('transform', 'transform')])])
+                        (copy_transform, intensity_correction, [('out_file', 'transform')])])
         
 
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")

From 3d60d7d51673e484c76d4052ad26609b9e5545bd Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 1 Apr 2016 15:09:19 -0500
Subject: [PATCH 22/72] FIX: adds item to outpus for autorecon1

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index 1979a5c235..d043115308 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -444,7 +444,7 @@ def awkfile(in_file, log_file):
                'braintemplate']
 
     if fsvernum < 6:
-        outputspec = pe.Node(IdentityInterface(fields=outputs + 'nu'),
+        outputspec = pe.Node(IdentityInterface(fields=outputs + ['nu']),
                              name="outputspec")
         ar1_wf.connect([(add_to_header_nu, outputspec, [('out_file', 'nu')])])
     else:

From 06d5fbc0b64cd29e49bcea69b871f88d0966459c Mon Sep 17 00:00:00 2001
From: David Ellis <dgellis90@gmail.com>
Date: Mon, 4 Apr 2016 09:13:57 -0500
Subject: [PATCH 23/72] FIX: Connects 'nu' of autorecon1 to autorecon2.

---
 nipype/workflows/smri/freesurfer/recon.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index e44091cdd9..e76d4e618a 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -258,7 +258,6 @@ def checkarg(arg, default):
                       (config_node, ar1_wf, [('reg_template_withskull',
                                               'inputspec.reg_template_withskull'),
                                              ('awk_file', 'inputspec.awk_file')])])
-
     # create AutoRecon2
     ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum)
     # connect inputs for AutoRecon2
@@ -269,6 +268,10 @@ def checkarg(arg, default):
                       (ar1_wf, ar2_wf, [('outputspec.brainmask', 'inputspec.brainmask'),
                                         ('outputspec.talairach', 'inputspec.transform'),
                                         ('outputspec.orig', 'inputspec.orig')])])
+
+    if fsvernum < 6:
+        reconall.connect([(ar1_wf, ar2_wf, [('outputspec.nu', 'inputspec.nu')])])
+
     # create AutoRecon3
     ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=th3,
                                             exvivo=exvivo, entorhinal=entorhinal)

From 759f52e3cc71ffb4d0bc3bac3e44348ebeed9a56 Mon Sep 17 00:00:00 2001
From: David Ellis <dgellis90@gmail.com>
Date: Mon, 4 Apr 2016 11:21:11 -0500
Subject: [PATCH 24/72] FIX: Takes out new inputs to CALabel.

---
 nipype/workflows/smri/freesurfer/autorecon2.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 955dbb93f2..3f1a2d1443 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -218,8 +218,9 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         fuse_segmentations.inputs.out_file = 'aseg.fused.mgz'
 
     ca_label = pe.Node(CALabel(), name='CA_Label')
-    ca_label.inputs.relabel_unlikely = (9, .3)
-    ca_label.inputs.prior = 0.5
+    if fsvernum > 6:
+        ca_label.inputs.relabel_unlikely = (9, .3)
+        ca_label.inputs.prior = 0.5
     ca_label.inputs.align = True
     ca_label.inputs.out_file = 'aseg.auto_noCCseg.mgz'
     if plugin_args:

From a6850cecaf8ca10897af91f0f840b022654ec1a4 Mon Sep 17 00:00:00 2001
From: David Ellis <dgellis90@gmail.com>
Date: Tue, 5 Apr 2016 08:31:25 -0500
Subject: [PATCH 25/72] FIX: Removes in_aseg from ribbon masking.

---
 nipype/interfaces/freesurfer/utils.py          |  3 ++-
 nipype/workflows/smri/freesurfer/autorecon3.py | 11 ++++++-----
 nipype/workflows/smri/freesurfer/recon.py      |  3 ++-
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 6edb1399e9..03f11e6d4b 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2363,7 +2363,8 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_pial, 'surf', 'rh.pial')
             copy2subjdir(self, self.inputs.lh_white, 'surf', 'lh.white')
             copy2subjdir(self, self.inputs.rh_white, 'surf', 'rh.white')
-            copy2subjdir(self, self.inputs.in_aseg, 'mri')
+            if isdefined(self.inputs.in_aseg):
+                copy2subjdir(self, self.inputs.in_aseg, 'mri')
         return super(VolumeMask, self).run(**inputs)
 
     def _format_arg(self, name, spec, value):
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index d0dc354677..13f60aeb9e 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -8,7 +8,7 @@
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
-                      th3=True, exvivo=True, entorhinal=True):
+                      th3=True, exvivo=True, entorhinal=True, fsvernum=5.3):
 
     # AutoRecon3
     # Workflow
@@ -274,14 +274,15 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
     volume_mask.inputs.copy_inputs = True
 
 
-    ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'in_aseg'),
-                                              ('lh_white', 'lh_white'),
-                                              ('rh_white', 'rh_white'),
-                                               ]),
+    ar3_wf.connect([(inputspec, volume_mask, [('lh_white', 'lh_white'),
+                                              ('rh_white', 'rh_white')]),
                     (ar3_lh_wf1, volume_mask, [('outputspec.pial', 'lh_pial')]),
                     (ar3_rh_wf1, volume_mask, [('outputspec.pial', 'rh_pial')]),
                     ])
 
+    if fsvernum > 6:
+        ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'in_aseg')])])
+
     ar3_lh_wf2 = pe.Workflow(name="AutoRecon3_Left_2")
     ar3_rh_wf2 = pe.Workflow(name="AutoRecon3_Right_2")
 
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index e76d4e618a..f6996b6f2a 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -274,7 +274,8 @@ def checkarg(arg, default):
 
     # create AutoRecon3
     ar3_wf, ar3_outputs = create_AutoRecon3(plugin_args=plugin_args, th3=th3,
-                                            exvivo=exvivo, entorhinal=entorhinal)
+                                            exvivo=exvivo, entorhinal=entorhinal,
+                                            fsvernum=fsvernum)
     # connect inputs for AutoRecon3
     reconall.connect([(config_node, ar3_wf, [('lh_atlas', 'inputspec.lh_atlas'),
                                              ('rh_atlas', 'inputspec.rh_atlas'),

From cd7dc15b266635ef63ff628a6be3e8c0c1a64ba9 Mon Sep 17 00:00:00 2001
From: David Ellis <dgellis90@gmail.com>
Date: Tue, 5 Apr 2016 09:05:20 -0500
Subject: [PATCH 26/72] ENH: Allows for implicit aseg input in ribbon masking.

---
 nipype/interfaces/freesurfer/utils.py         | 27 ++++++++++++++-----
 .../workflows/smri/freesurfer/autorecon3.py   |  2 ++
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 03f11e6d4b..9ba8256fa6 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -35,21 +35,30 @@
 
 
 def copy2subjdir(cls, in_file, folder=None, basename=None, subject_id=None):
+    """Method to copy an input to the subjects directory"""
+    # check that the input is defined
+    if not isdefined(in_file):
+        return in_file
+    # check that subjects_dir is defined
     if isdefined(cls.inputs.subjects_dir):
         subjects_dir = cls.inputs.subjects_dir
     else:
-        subjects_dir = os.getcwd()
+        subjects_dir = os.getcwd() #if not use cwd
+    # check for subject_id
     if not subject_id:
         if isdefined(cls.inputs.subject_id):
             subject_id = cls.inputs.subject_id
         else:
-            subject_id = 'subject_id'
+            subject_id = 'subject_id' #default
+    # check for basename
     if basename == None:
         basename = os.path.basename(in_file)
+    # check which folder to put the file in
     if folder != None:
         out_dir = os.path.join(subjects_dir, subject_id, folder)
     else:
         out_dir = os.path.join(subjects_dir, subject_id)
+    # make the output folder if it does not exist
     if not os.path.isdir(out_dir):
         os.makedirs(out_dir)
     out_file = os.path.join(out_dir, basename)
@@ -58,7 +67,7 @@ def copy2subjdir(cls, in_file, folder=None, basename=None, subject_id=None):
     return out_file
 
 def createoutputdirs(outputs):
-    """create an output directories. If not created, some freesurfer interfaces fail"""
+    """create all output directories. If not created, some freesurfer interfaces fail"""
     for output in outputs.itervalues():
         dirname = os.path.dirname(output)
         if not os.path.isdir(dirname):
@@ -2301,11 +2310,16 @@ class VolumeMaskInputSpec(FSTraitedSpec):
                     desc="Implicit input left white matter surface")
     rh_white = File(mandatory=True, exists=True,
                     desc="Implicit input right white matter surface")
+    aseg = File(mandatory=True, exists=True,
+                xor=['in_aseg'], 
+                desc="Implicit aseg.mgz segmentation. " + 
+                "Specify a different aseg by using the 'in_aseg' input.")
     subject_id = traits.String('subject_id', usedefault=True,
                                position=-1, argstr="%s", mandatory=True,
                                desc="Subject being processed")
     # optional
-    in_aseg = File(argstr="--aseg_name %s", mandatory=False, exists=True,
+    in_aseg = File(argstr="--aseg_name %s", mandatory=False, 
+                   exists=True, xor=['aseg'],
                    desc="Input aseg file for VolumeMask")
     save_ribbon = traits.Bool(argstr="--save_ribbon", mandatory=False,
                               desc="option to save just the ribbon for the " +
@@ -2363,8 +2377,9 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_pial, 'surf', 'rh.pial')
             copy2subjdir(self, self.inputs.lh_white, 'surf', 'lh.white')
             copy2subjdir(self, self.inputs.rh_white, 'surf', 'rh.white')
-            if isdefined(self.inputs.in_aseg):
-                copy2subjdir(self, self.inputs.in_aseg, 'mri')
+            copy2subjdir(self, self.inputs.in_aseg, 'mri')
+            copy2subjdir(self, self.inputs.aseg, 'mri', 'aseg.mgz')
+            
         return super(VolumeMask, self).run(**inputs)
 
     def _format_arg(self, name, spec, value):
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 13f60aeb9e..6f31020273 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -282,6 +282,8 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
 
     if fsvernum > 6:
         ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'in_aseg')])])
+    else:
+        ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'aseg')])])
 
     ar3_lh_wf2 = pe.Workflow(name="AutoRecon3_Left_2")
     ar3_rh_wf2 = pe.Workflow(name="AutoRecon3_Right_2")

From c0cf40f488d423da8bd0799ef93b35536df85204 Mon Sep 17 00:00:00 2001
From: David Ellis <dgellis90@gmail.com>
Date: Tue, 5 Apr 2016 09:07:17 -0500
Subject: [PATCH 27/72] FIX: Fixes typo.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 6f31020273..4b57b8790a 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -281,9 +281,9 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     ])
 
     if fsvernum > 6:
-        ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'in_aseg')])])
+        ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'in_aseg')])])
     else:
-        ar3_wf.connect([(inputpsec, volume_mask, [('aseg_presurf', 'aseg')])])
+        ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'aseg')])])
 
     ar3_lh_wf2 = pe.Workflow(name="AutoRecon3_Left_2")
     ar3_rh_wf2 = pe.Workflow(name="AutoRecon3_Right_2")

From 37fd56cab34da3e91f50abf7bdfb833d97bdd6b4 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 12:41:56 -0500
Subject: [PATCH 28/72] FIX: Fixes source subject for BAMaps thresh.

---
 nipype/workflows/smri/freesurfer/ba_maps.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index a8054e9669..25f7c148c9 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -65,6 +65,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                                   white='surf/{0}.white'.format(hemisphere))
 
             out_files = list()
+            source_fields = ['sphere_reg', 'white']
             if threshold:
                 for label in labels:
                     if label == 'perirhinal' and not entorhinal:
@@ -76,7 +77,8 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                         out_file = '{0}.{1}.thresh.label'.format(hemisphere, label)
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
-                node_name = 'BA_Maps_' + hemisphere + '_Tresh'
+                    source_fields.append(label)
+                node_name = 'BA_Maps_' + hemisphere + '_Thresh'
             else:
                 for label in labels:
                     if exvivo:
@@ -86,9 +88,9 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                         
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
+                    source_fields.append(label)
                 node_name = 'BA_Maps_' + hemisphere
 
-            source_fields = labels + ['sphere_reg', 'white']
             source_subject = pe.Node(DataGrabber(outfields=source_fields),
                                      name=node_name + "_srcsubject")
             source_subject.inputs.template = '*'
@@ -96,7 +98,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
             source_subject.inputs.field_template = field_template
             ba_WF.connect([(inputspec, source_subject, [('src_subject_dir', 'base_directory')])])
 
-            merge_labels = pe.Node(Merge(len(labels)),
+            merge_labels = pe.Node(Merge(len(out_files)),
                                    name=node_name + "_Merge")
             for i,label in enumerate(labels):
                 ba_WF.connect([(source_subject, merge_labels, [(label, 'in{0}'.format(i+1))])])

From 1b95329ced63920f06aa068d40409c9d1456fecb Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 12:54:46 -0500
Subject: [PATCH 29/72] FIX: Temporary fix for apas2aseg. Will still need to
 fix what is going wrong with aseg.mgz.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 4b57b8790a..19406678d5 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -6,6 +6,7 @@
 from .ba_maps import create_ba_maps_wf
 from .utils import createsrcsubj
 from nipype.interfaces.io import DataGrabber
+from .utils import copy_file
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                       th3=True, exvivo=True, entorhinal=True, fsvernum=5.3):
@@ -600,9 +601,17 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (relabel_hypos, aparc_2_aseg_2009, [('out_file', 'aseg')])
                     ])
 
-    apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
+    if fsvernum > 6:
+        apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
+    else:
+        apas_2_aseg = pe.Node(Function(['in_file', 'out_file'],
+                                       ['out_file'],
+                                       copy_file),
+                              name="Copy2Aseg")
+        
+    ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
     apas_2_aseg.inputs.out_file = "aseg.mgz"
-    ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])
+                                       
 
     # Segmentation Stats
     """

From 2daa8c19080735c329adfaa8f7d7d72f4d8482aa Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 13:02:05 -0500
Subject: [PATCH 30/72] FIX: Changes reference of labels to source_fields.

---
 nipype/workflows/smri/freesurfer/ba_maps.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 25f7c148c9..21847226bd 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -100,7 +100,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
 
             merge_labels = pe.Node(Merge(len(out_files)),
                                    name=node_name + "_Merge")
-            for i,label in enumerate(labels):
+            for i,label in enumerate(source_fields):
                 ba_WF.connect([(source_subject, merge_labels, [(label, 'in{0}'.format(i+1))])])
 
             node = pe.MapNode(Label2Label(), name=node_name,

From 25b7e962b59742ba9571f48c406d20543427c7bb Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 13:34:07 -0500
Subject: [PATCH 31/72] Fix: turns the mandatory flag off for aseg.

---
 nipype/interfaces/freesurfer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 9ba8256fa6..2d1da1b78c 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2310,7 +2310,7 @@ class VolumeMaskInputSpec(FSTraitedSpec):
                     desc="Implicit input left white matter surface")
     rh_white = File(mandatory=True, exists=True,
                     desc="Implicit input right white matter surface")
-    aseg = File(mandatory=True, exists=True,
+    aseg = File(exists=True,
                 xor=['in_aseg'], 
                 desc="Implicit aseg.mgz segmentation. " + 
                 "Specify a different aseg by using the 'in_aseg' input.")

From ac600650edfa34b2b992bdf27e34fdeff22a2ce5 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 13:44:57 -0500
Subject: [PATCH 32/72] FIX: Fixes failure to copy rh.white

---
 nipype/interfaces/freesurfer/model.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
index 2980f147d8..7c9ba8bb68 100644
--- a/nipype/interfaces/freesurfer/model.py
+++ b/nipype/interfaces/freesurfer/model.py
@@ -859,7 +859,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.lh_white,
                          'surf', 'lh.white')
             copy2subjdir(self, self.inputs.rh_white,
-                         'Surf', 'Rh.White')
+                         'surf', 'rh.white')
             copy2subjdir(self, self.inputs.lh_pial,
                          'surf', 'lh.pial')
             copy2subjdir(self, self.inputs.rh_pial,
@@ -872,8 +872,7 @@ def run(self, **inputs):
                          os.path.join('mri', 'transforms'),
                          'talairach.xfm')
             copy2subjdir(self, self.inputs.in_intensity, 'mri')
-            if isdefined(self.inputs.brainmask_file):
-                copy2subjdir(self, self.inputs.brainmask_file, 'mri')
+            copy2subjdir(self, self.inputs.brainmask_file, 'mri')
         return super(SegStatsReconAll, self).run(**inputs)
 
 

From d6560f1b837ae600253638b24225f1e1f39cf090 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 13:51:46 -0500
Subject: [PATCH 33/72] FIX: Adds filled input to Aparc2Aseg.

---
 nipype/interfaces/freesurfer/utils.py          | 3 +++
 nipype/workflows/smri/freesurfer/autorecon3.py | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 2d1da1b78c..016655c032 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2742,6 +2742,8 @@ class Aparc2AsegInputSpec(FSTraitedSpec):
     rh_annotation = File(mandatory=True, exists=True,
                          desc="Input file must be <subject_id>/label/rh.aparc.annot")
     # optional
+    filled = File(exists=True,
+                  desc="Implicit input filled file. Only required with FS v5.3.")
     aseg = File(argstr="--aseg %s", mandatory=False, exists=True,
                 desc="Input aseg file")
     volmask = traits.Bool(argstr="--volmask", mandatory=False,
@@ -2824,6 +2826,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_ribbon, 'mri', 'rh.ribbon.mgz')
             copy2subjdir(self, self.inputs.ribbon, 'mri', 'ribbon.mgz')
             copy2subjdir(self, self.inputs.aseg, 'mri')
+            copy2subjdir(self, self.inputs.filled, 'mri', 'filled.mgz')
             copy2subjdir(self, self.inputs.lh_annotation, 'label')
             copy2subjdir(self, self.inputs.rh_annotation, 'label')
 
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 19406678d5..b4b5162693 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -685,6 +685,9 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (aparc_2_aseg, wm_parcellation, [('out_file', 'ctxseg')])
                     ])
 
+    if fsvernum < 6:
+        ar3_wf.connect([(inputspec, wm_parcellation, [('filled', 'filled')])])
+
     # White Matter Segmentation Stats
 
     wm_segstats = pe.Node(SegStatsReconAll(), name="WM_Segmentation_Statistics")

From 9057ffa64b8c434795285b4a4291a8f4a04e8798 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 14:11:07 -0500
Subject: [PATCH 34/72] FIX: Allows for aseg to be copied in segstats for 5.3.

---
 nipype/interfaces/freesurfer/model.py          | 4 ++++
 nipype/workflows/smri/freesurfer/autorecon3.py | 7 ++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
index 7c9ba8bb68..f09ca64b8f 100644
--- a/nipype/interfaces/freesurfer/model.py
+++ b/nipype/interfaces/freesurfer/model.py
@@ -796,6 +796,8 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
                    desc="Input file must be <subject_id>/surf/lh.pial")
     rh_pial = File(mandatory=True, exists=True,
                    desc="Input file must be <subject_id>/surf/rh.pial")
+    aseg = File(exists=True,
+                desc="Mandatory implicit input in 5.3")
     copy_inputs = traits.Bool(desc="If running as a node, set this to True " +
                               "otherwise, this will copy the implicit inputs " +
                               "to the node directory.")
@@ -868,6 +870,8 @@ def run(self, **inputs):
                          'mri', 'ribbon.mgz')
             copy2subjdir(self, self.inputs.presurf_seg,
                          'mri', 'aseg.presurf.mgz')
+            copy2subjdir(self, self.inputs.aseg,
+                         'mri', 'aseg.mgz')
             copy2subjdir(self, self.inputs.transform,
                          os.path.join('mri', 'transforms'),
                          'talairach.xfm')
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index b4b5162693..ed97153995 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -638,7 +638,6 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
     ar3_wf.connect([(apas_2_aseg, segstats, [('out_file', 'segmentation_file')]),
                     (inputspec, segstats, [('lh_white', 'lh_white'),
                                            ('rh_white', 'rh_white'),
-                                           ('aseg_presurf', 'presurf_seg'),
                                            ('transform', 'transform'),
                                            ('norm', 'in_intensity'),
                                            ('norm', 'partial_volume_file'),
@@ -654,6 +653,12 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                                            ]),
                     ])
 
+    if fsvernum > 6:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'presurf_seg')
+    else:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'aseg')
+
+
     # White Matter Parcellation
 
     # Adds WM Parcellation info into the aseg and computes stat.

From 1ec5bf0cb11ab406bc2968673190722a28360e6f Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 16:11:00 -0500
Subject: [PATCH 35/72] FIX: Changes presurf_seg to not being mandatory.

---
 nipype/interfaces/freesurfer/model.py       | 2 +-
 nipype/workflows/smri/freesurfer/ba_maps.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py
index f09ca64b8f..5196292835 100644
--- a/nipype/interfaces/freesurfer/model.py
+++ b/nipype/interfaces/freesurfer/model.py
@@ -780,7 +780,7 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
     # implicit
     ribbon = traits.File(mandatory=True, exists=True,
                          desc="Input file mri/ribbon.mgz")
-    presurf_seg = File(mandatory=True, exists=True,
+    presurf_seg = File(exists=True,
                        desc="Input segmentation volume")
     transform = File(mandatory=True, exists=True,
                      desc="Input transform file")
diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 21847226bd..2d7a1ea41b 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -103,7 +103,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
             for i,label in enumerate(source_fields):
                 ba_WF.connect([(source_subject, merge_labels, [(label, 'in{0}'.format(i+1))])])
 
-            node = pe.MapNode(Label2Label(), name=node_name,
+            node = pe.MapNode(Label2Label(), name=node_name + '_Label2Label',
                               iterfield=['source_label', 'out_file'])
             node.inputs.hemisphere = hemisphere
             node.inputs.out_file = out_files

From 0b6eb84be7d10c491cee9e3c6b01e3c8f97a45af Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 16:12:45 -0500
Subject: [PATCH 36/72] FIX: Updates WM_Parcellation_Stats to take aseg as
 input.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index ed97153995..7d1ad252a8 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -724,6 +724,13 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                                               ]),
                     ])
 
+    if fsvernum > 6:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'presurf_seg')
+    else:
+        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'aseg')
+
+
+
     # add brodman area maps to the workflow
     ba_WF, ba_outputs = create_ba_maps_wf(th3=th3, exvivo=exvivo,
                                           entorhinal=entorhinal)

From 987427aec06725eaa5cf283a2bc82138c46b0f1d Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 16:14:35 -0500
Subject: [PATCH 37/72] FIX: Fixes typo when connecting workflows.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 7d1ad252a8..0411a41907 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -725,9 +725,9 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     ])
 
     if fsvernum > 6:
-        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'presurf_seg')
+        ar3_wf.connect(inputspec, 'aseg_presurf', wm_segstats, 'presurf_seg')
     else:
-        ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'aseg')
+        ar3_wf.connect(inputspec, 'aseg_presurf', wm_segstats, 'aseg')
 
 
 

From 2c1c045a630597b5db977b6e62b91e5bbfbc4dc9 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 6 Apr 2016 16:41:34 -0500
Subject: [PATCH 38/72] FIX: Fixes error causing sphere.reg to be passed as a
 label.

---
 nipype/workflows/smri/freesurfer/ba_maps.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 2d7a1ea41b..34c978c102 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -65,7 +65,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                                   white='surf/{0}.white'.format(hemisphere))
 
             out_files = list()
-            source_fields = ['sphere_reg', 'white']
+            source_fields = list()
             if threshold:
                 for label in labels:
                     if label == 'perirhinal' and not entorhinal:
@@ -91,7 +91,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                     source_fields.append(label)
                 node_name = 'BA_Maps_' + hemisphere
 
-            source_subject = pe.Node(DataGrabber(outfields=source_fields),
+            source_subject = pe.Node(DataGrabber(outfields=source_fields + ['sphere_reg', 'white']),
                                      name=node_name + "_srcsubject")
             source_subject.inputs.template = '*'
             source_subject.inputs.sort_filelist = False

From ce8a0df2d164d46f496ff6d78450b9057a40b8d2 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Thu, 7 Apr 2016 10:15:15 -0500
Subject: [PATCH 39/72] FIX: Changes orig_nu.mgz to nu.mgz for the input to
 EM_register.

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index d043115308..d43121077f 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -386,8 +386,12 @@ def awkfile(in_file, log_file):
         if plugin_args:
             mri_em_register.plugin_args = plugin_args
 
-        ar1_wf.connect([(add_xform_to_orig_nu, mri_em_register, [('out_file', 'in_file')]),
-                        (inputspec, mri_em_register, [('num_threads', 'num_threads'),
+        if fsvernum < 6:
+            ar1_wf.connect(add_to_header_nu, 'out_file', mri_em_register, 'in_file')
+        else:
+            ar1_wf.connect(add_xform_to_orig_nu, 'out_file', mri_em_register, 'in_file')
+            
+        ar1_wf.connect([(inputspec, mri_em_register, [('num_threads', 'num_threads'),
                                                       ('reg_template_withskull', 'template')])])
 
         brainmask = pe.Node(WatershedSkullStrip(),

From 7959d40c4e57cd9525dd353a0a87353423af044c Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 11:56:35 -0500
Subject: [PATCH 40/72] ENH: Makes mris_make_surfaces compatable with the 5.3
 recon-all.

---
 nipype/interfaces/freesurfer/utils.py         | 15 ++++++------
 .../workflows/smri/freesurfer/autorecon2.py   | 13 ++++++++--
 .../workflows/smri/freesurfer/autorecon3.py   | 24 ++++++++++++++-----
 3 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 016655c032..ca5a207e4e 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -1902,6 +1902,8 @@ class MakeSurfacesInputSpec(FSTraitedSpec):
         argstr="-max %.1f", desc="No documentation (used for longitudinal processing)")
     longitudinal = traits.Bool(
         argstr="-long", desc="No documentation (used for longitudinal processing)")
+    white = traits.String(argstr="-white %s",
+                          desc="White surface name")
     copy_inputs = traits.Bool(mandatory=False,
                               desc="If running as a node, set this to True." +
                               "This will copy the input files to the node " +
@@ -1958,13 +1960,11 @@ def run(self, **inputs):
                          folder='mri', basename='filled.mgz')
             for originalfile in [self.inputs.in_aseg,
                                  self.inputs.in_T1]:
-                if isdefined(originalfile):
-                    copy2subjdir(self, originalfile, folder='mri')
+                copy2subjdir(self, originalfile, folder='mri')
             for originalfile in [self.inputs.orig_white,
                                  self.inputs.orig_pial,
                                  self.inputs.in_orig]:
-                if isdefined(originalfile):
-                    copy2subjdir(self, originalfile, folder='surf')
+                copy2subjdir(self, originalfile, folder='surf')
             if isdefined(self.inputs.in_label):
                 copy2subjdir(self, self.inputs.in_label, 'label',
                              '{0}.aparc.annot'.format(self.inputs.hemisphere))
@@ -1981,9 +1981,11 @@ def _format_arg(self, name, spec, value):
             basename = os.path.basename(value)
             # whent the -mgz flag is specified, it assumes the mgz extension
             if self.inputs.mgz:
-                prefix = basename.rstrip('.mgz')
+                prefix = value.rstrip('.mgz')
             else:
                 prefix = basename
+            if prefix == 'aseg':
+                return # aseg is already the default
             return spec.argstr % prefix
         elif name in ['orig_white', 'orig_pial']:
             # these inputs do take full file paths or even basenames
@@ -2038,7 +2040,7 @@ def _list_outputs(self):
 
 class CurvatureInputSpec(FSTraitedSpec):
     in_file = File(argstr="%s", position=-2, mandatory=True, exists=True,
-                   desc="Input file for Curvature")
+                   copyfile=True, desc="Input file for Curvature")
     # optional
     threshold = traits.Float(
         argstr="-thresh %.3f", mandatory=False, desc="Undocumented input threshold")
@@ -2082,7 +2084,6 @@ def _format_arg(self, name, spec, value):
         if self.inputs.copy_input:
             if name == 'in_file':
                 basename = os.path.basename(value)
-                shutil.copy(value, basename)
                 return spec.argstr % basename
         return super(Curvature, self)._format_arg(name, spec, value)
 
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 3f1a2d1443..273994d9d5 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -156,8 +156,14 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
     else:
         ca_register.inputs.levels = 2
         ca_register.inputs.A = 1
-        ar2_wf.connect([(ar1_inputs, ca_register, [('template_talairach_m3z', 'l_files')])])
+        ar2_wf.connect([(inputspec, ca_register, [('template_talairach_m3z', 'l_files')])])
 
+
+    if fsvernum < 6:
+        # 5.3 runs two ca_register steps
+        ca_register2 = pe.Node(CARegister(), name='CA_Register2')
+        ca_register2.inputs.invert_and_save = True
+        ar2_wf.connect(ca_register, 'out_file', ca_register2, '')
     # Remove Neck
     """
     The neck region is removed from the NU-corrected volume mri/nu.mgz. Makes use
@@ -248,7 +254,10 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
                                ['out_file'],
                                copy_file),
                       name='Copy_CCSegmentation')
-    copy_cc.inputs.out_file = 'aseg.presurf.mgz'
+    if fsvernum > 6:
+        copy_cc.inputs.out_file = 'aseg.presurf.mgz'
+    else:
+        copy_cc.inputs.out_file = 'aseg.mgz'
 
     ar2_wf.connect([(segment_cc, copy_cc, [('out_file', 'in_file')])
                     ])
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 0411a41907..b62c8a504f 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -166,11 +166,19 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # Pial Surface
 
         ar3_pial = pe.Node(MakeSurfaces(), name="Make_Pial_Surface")
-        ar3_pial.inputs.no_white = True
         ar3_pial.inputs.mgz = True
         ar3_pial.inputs.hemisphere = hemisphere
         ar3_pial.inputs.copy_inputs = True
 
+
+        if fsvernum < 6:
+            hemi_wf.connect(hemi_inputspec1, 'white', ar3_pial, 'in_white')
+            ar3_pial.inputs.white = 'NOWRITE'
+        else:
+            ar3_pial.inputs.no_white = True
+            hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('white', 'orig_pial'),
+                                                          ('white', 'orig_white')])])
+
         hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('wm', 'in_wm'),
                                                       ('orig', 'in_orig'),
                                                       ('filled', 'in_filled'),
@@ -603,13 +611,17 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
 
     if fsvernum > 6:
         apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
+        ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
     else:
-        apas_2_aseg = pe.Node(Function(['in_file', 'out_file'],
+        # aseg.mgz gets edited in place, so we'll copy and pass it to the
+        # outputspec once aparc_2_aseg has completed
+        def out_aseg(in_aparcaseg, in_aseg, out_file):
+            out_file = copy_file(in_aseg, out_file)
+            return out_file
+        apas_2_aseg = pe.Node(Function(['in_aparcaseg', 'in_aseg', 'out_file'],
                                        ['out_file'],
-                                       copy_file),
-                              name="Copy2Aseg")
-        
-    ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
+                                       out_aseg),
+                              name="Aseg")
     apas_2_aseg.inputs.out_file = "aseg.mgz"
                                        
 

From 2c9cb25abfa9a54db01e52e7f9f01f7d5bf792b9 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 12:02:25 -0500
Subject: [PATCH 41/72] FIX: Removes unnecessary step in autorecon2.

---
 nipype/workflows/smri/freesurfer/autorecon2.py | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 273994d9d5..c616114fab 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -158,12 +158,6 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         ca_register.inputs.A = 1
         ar2_wf.connect([(inputspec, ca_register, [('template_talairach_m3z', 'l_files')])])
 
-
-    if fsvernum < 6:
-        # 5.3 runs two ca_register steps
-        ca_register2 = pe.Node(CARegister(), name='CA_Register2')
-        ca_register2.inputs.invert_and_save = True
-        ar2_wf.connect(ca_register, 'out_file', ca_register2, '')
     # Remove Neck
     """
     The neck region is removed from the NU-corrected volume mri/nu.mgz. Makes use

From 490446e6ff3b0dfd13335f2cad5914fad6eeab9e Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 12:07:36 -0500
Subject: [PATCH 42/72] ENH: Adds in_white to Make Surfaces.

---
 nipype/interfaces/freesurfer/utils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index ca5a207e4e..4dfd428945 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -1876,6 +1876,7 @@ class MakeSurfacesInputSpec(FSTraitedSpec):
     in_filled = File(exists=True, mandatory=True,
                      desc="Implicit input file filled.mgz")
     # optional
+    in_white = File(exists=True, desc="Implicit input that is sometimes used")
     in_label = File(exists=True, mandatory=False, xor=['noaparc'],
                     desc="Implicit input label/<hemisphere>.aparc.annot")
     orig_white = File(argstr="-orig_white %s", exists=True, mandatory=False,
@@ -1958,6 +1959,8 @@ def run(self, **inputs):
                          folder='mri', basename='wm.mgz')
             copy2subjdir(self, self.inputs.in_filled,
                          folder='mri', basename='filled.mgz')
+            copy2subjdir(self, self.inputs.in_white,
+                         'surf', '{0}.white'.format(self.inputs.hemisphere))
             for originalfile in [self.inputs.in_aseg,
                                  self.inputs.in_T1]:
                 copy2subjdir(self, originalfile, folder='mri')

From e262e78dd2d2b47532cbd728e306af3d0b4445fd Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 12:58:15 -0500
Subject: [PATCH 43/72] FIX: Switches the format of arguments for
 mris_make_surfaces to basename for input images.

---
 nipype/interfaces/freesurfer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 4dfd428945..c5ee985c66 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -1984,7 +1984,7 @@ def _format_arg(self, name, spec, value):
             basename = os.path.basename(value)
             # whent the -mgz flag is specified, it assumes the mgz extension
             if self.inputs.mgz:
-                prefix = value.rstrip('.mgz')
+                prefix = basename.rstrip('.mgz')
             else:
                 prefix = basename
             if prefix == 'aseg':

From 5060fdc56bc6dbb84f6069fa70f2fc3ed5a029cc Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 13:03:15 -0500
Subject: [PATCH 44/72] FIX: Adds inputs to the copying of aseg_presurf to
 aseg.mgz.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index b62c8a504f..c9ed659546 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -622,6 +622,9 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                        ['out_file'],
                                        out_aseg),
                               name="Aseg")
+        ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_aparcaseg')]),
+                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])       
+
     apas_2_aseg.inputs.out_file = "aseg.mgz"
                                        
 

From 6c63ded2f2c1a71ab21249b69c5d2488401e54a6 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 13:10:34 -0500
Subject: [PATCH 45/72] FIX: Changes .rsplit to os.path.splittext.

---
 nipype/interfaces/freesurfer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index c5ee985c66..03e1ab1a3b 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -1984,7 +1984,7 @@ def _format_arg(self, name, spec, value):
             basename = os.path.basename(value)
             # whent the -mgz flag is specified, it assumes the mgz extension
             if self.inputs.mgz:
-                prefix = basename.rstrip('.mgz')
+                prefix = os.path.splitext(basename)[0]
             else:
                 prefix = basename
             if prefix == 'aseg':

From 848442bb40368b7e16a63c1023ad3d0bc2ec61fa Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Mon, 11 Apr 2016 13:58:22 -0500
Subject: [PATCH 46/72] FIX: Removes the unnecessary inputs to MakeSurfaces for
 53.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index c9ed659546..56d1890e8c 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -172,8 +172,8 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
 
 
         if fsvernum < 6:
-            hemi_wf.connect(hemi_inputspec1, 'white', ar3_pial, 'in_white')
             ar3_pial.inputs.white = 'NOWRITE'
+            hemi_wf.connect(hemi_inputspec1, 'white', ar3_pial, 'in_white')
         else:
             ar3_pial.inputs.no_white = True
             hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('white', 'orig_pial'),
@@ -182,8 +182,6 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         hemi_wf.connect([(hemi_inputspec1, ar3_pial, [('wm', 'in_wm'),
                                                       ('orig', 'in_orig'),
                                                       ('filled', 'in_filled'),
-                                                      ('white', 'orig_pial'),
-                                                      ('white', 'orig_white'),
                                                       ('brain_finalsurfs', 'in_T1'),
                                                       ('aseg_presurf', 'in_aseg')]),
                          (ar3_parcellation, ar3_pial, [('out_file', 'in_label')])

From 1857064952b5bac9f7ac7775838116ff78f70338 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 10:05:15 -0500
Subject: [PATCH 47/72] FIX: Allows the interface wrapper to know it is making
 a pial surface for 5.3.0.

---
 nipype/interfaces/freesurfer/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 03e1ab1a3b..8ef75478f1 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2025,8 +2025,8 @@ def _list_outputs(self):
             dest_dir, str(self.inputs.hemisphere) + '.area')
         # Something determines when a pial surface and thickness file is generated
         # but documentation doesn't say what.
-        # The orig_pial flag is just a guess
-        if isdefined(self.inputs.orig_pial):
+        # The orig_pial input is just a guess
+        if isdefined(self.inputs.orig_pial) or self.inputs.white == 'NOWRITE':
             outputs["out_curv"] = outputs["out_curv"] + ".pial"
             outputs["out_area"] = outputs["out_area"] + ".pial"
             outputs["out_pial"] = os.path.join(

From ede459f57531651964d4f24d72c6430bb30b3c99 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 11:02:54 -0500
Subject: [PATCH 48/72] FIX: Adds import statement to output aseg function.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 56d1890e8c..016f5880fa 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -614,6 +614,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # aseg.mgz gets edited in place, so we'll copy and pass it to the
         # outputspec once aparc_2_aseg has completed
         def out_aseg(in_aparcaseg, in_aseg, out_file):
+            from .utils import copy_file
             out_file = copy_file(in_aseg, out_file)
             return out_file
         apas_2_aseg = pe.Node(Function(['in_aparcaseg', 'in_aseg', 'out_file'],

From a2672c835eb2afd14267256496c16f274fa7b516 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 11:10:50 -0500
Subject: [PATCH 49/72] FIX: Fixes import statement.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 016f5880fa..893836442d 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -614,7 +614,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # aseg.mgz gets edited in place, so we'll copy and pass it to the
         # outputspec once aparc_2_aseg has completed
         def out_aseg(in_aparcaseg, in_aseg, out_file):
-            from .utils import copy_file
+            import copy_file
             out_file = copy_file(in_aseg, out_file)
             return out_file
         apas_2_aseg = pe.Node(Function(['in_aparcaseg', 'in_aseg', 'out_file'],

From 775f1f9b6637e30c832b6ae80322be21ed5af6bd Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 11:19:27 -0500
Subject: [PATCH 50/72] FIX: Adds shutil to import for out_aseg function.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 893836442d..02337e98d2 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -614,8 +614,9 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # aseg.mgz gets edited in place, so we'll copy and pass it to the
         # outputspec once aparc_2_aseg has completed
         def out_aseg(in_aparcaseg, in_aseg, out_file):
-            import copy_file
-            out_file = copy_file(in_aseg, out_file)
+            import shutil
+            out_file = os.path.abspath(out_file)
+            shutil.copy(in_aseg, out_file)
             return out_file
         apas_2_aseg = pe.Node(Function(['in_aparcaseg', 'in_aseg', 'out_file'],
                                        ['out_file'],

From 44f1e29dc54c6cf1ff4af588fe63700096e4ae92 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 11:26:25 -0500
Subject: [PATCH 51/72] FIX: Imports os for out_aseg function.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 02337e98d2..ad1cff1498 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -6,7 +6,6 @@
 from .ba_maps import create_ba_maps_wf
 from .utils import createsrcsubj
 from nipype.interfaces.io import DataGrabber
-from .utils import copy_file
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                       th3=True, exvivo=True, entorhinal=True, fsvernum=5.3):
@@ -615,6 +614,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         # outputspec once aparc_2_aseg has completed
         def out_aseg(in_aparcaseg, in_aseg, out_file):
             import shutil
+            import os
             out_file = os.path.abspath(out_file)
             shutil.copy(in_aseg, out_file)
             return out_file

From 022352c9ad14c1104d775bba0478d3c2cbba4126 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 15:57:19 -0500
Subject: [PATCH 52/72] FIX: fixes bugs in recoding table workflow.

---
 nipype/workflows/smri/freesurfer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 69eb22911e..b2d9d721ce 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -568,7 +568,7 @@ def minimizeSizeOfImage(outlabels):
 
 
 def create_recoding_wf(in_file, out_file=None):
-    wf = nipype.Workflow(name="RecodeLabels")
+    wf = pe.Workflow(name="RecodeLabels")
 
     inputspec = nipype.pipeline.Node(nipype.IdentityInterface(['labelmap',
                                                                'recode_file']),

From f3acecc1b4443296c27eb17ef4de58d716fbeab8 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 16:00:46 -0500
Subject: [PATCH 53/72] FIX: Changes nipype.pipeline.Node to pe.Node

---
 nipype/workflows/smri/freesurfer/utils.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index b2d9d721ce..94988865bf 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -570,12 +570,12 @@ def minimizeSizeOfImage(outlabels):
 def create_recoding_wf(in_file, out_file=None):
     wf = pe.Workflow(name="RecodeLabels")
 
-    inputspec = nipype.pipeline.Node(nipype.IdentityInterface(['labelmap',
-                                                               'recode_file']),
-                                     name="inputspec")
+    inputspec = pe.Node(niu.IdentityInterface(['labelmap',
+                                               'recode_file']),
+                        name="inputspec")
     inputspec.inputs.recode_file = in_file
 
-    convert_labelmap = nipype.pipeline.Node(fs.MRIConvert(), name="ConvertLabelMap")
+    convert_labelmap = pe.Node(fs.MRIConvert(), name="ConvertLabelMap")
     convert_labelmap.inputs.in_type = 'mgz'
     convert_labelmap.inputs.out_type = 'nii'
     convert_labelmap.inputs.out_orientation = 'RAS'

From 7050d576a220dd907d01af5b9a81e97806143335 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 16:06:15 -0500
Subject: [PATCH 54/72] FIX: Changes nipype.Node to pe.Node.

---
 nipype/workflows/smri/freesurfer/utils.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 94988865bf..4f2f81f62a 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -582,7 +582,7 @@ def create_recoding_wf(in_file, out_file=None):
     convert_labelmap.inputs.out_file = 'labelmap.nii'
     wf.connect([(inputspec, convert_labelmap, [('labelmap', 'in_file')])])
 
-    recode = nipype.Node(nipype.Function(['in_file',
+    recode = pe.Node(nipype.Function(['in_file',
                                           'out_file',
                                           'recode_file'],
                                          ['out_file'],
@@ -596,13 +596,13 @@ def create_recoding_wf(in_file, out_file=None):
     wf.connect([(convert_labelmap, recode, [('out_file', 'in_file')]),
                 (inputspec, recode, [('recode_file', 'recode_file')])])
 
-    center_labelmap = nipype.Node(nipype.Function(['in_file'], ['out_file'],
+    center_labelmap = pe.Node(nipype.Function(['in_file'], ['out_file'],
                                                   center_volume),
                                   name="CenterLabelMap")
 
     wf.connect([(recode, center_labelmap, [('out_file', 'in_file')])])
 
-    outputspec = nipype.Node(nipype.IdentityInterface(['recodedlabelmap']), name="outputspec")
+    outputspec = pe.Node(nipype.IdentityInterface(['recodedlabelmap']), name="outputspec")
 
     wf.connect([(center_labelmap, outputspec, [('out_file', 'recodedlabelmap')])])
     return wf

From ccb4b164c71417334644be173eec60b3b25bb45d Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 16:12:55 -0500
Subject: [PATCH 55/72] FIX: Changes nipype.Function to Function.

---
 nipype/workflows/smri/freesurfer/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 4f2f81f62a..c9a530eb4b 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -582,7 +582,7 @@ def create_recoding_wf(in_file, out_file=None):
     convert_labelmap.inputs.out_file = 'labelmap.nii'
     wf.connect([(inputspec, convert_labelmap, [('labelmap', 'in_file')])])
 
-    recode = pe.Node(nipype.Function(['in_file',
+    recode = pe.Node(Function(['in_file',
                                           'out_file',
                                           'recode_file'],
                                          ['out_file'],
@@ -596,7 +596,7 @@ def create_recoding_wf(in_file, out_file=None):
     wf.connect([(convert_labelmap, recode, [('out_file', 'in_file')]),
                 (inputspec, recode, [('recode_file', 'recode_file')])])
 
-    center_labelmap = pe.Node(nipype.Function(['in_file'], ['out_file'],
+    center_labelmap = pe.Node(Function(['in_file'], ['out_file'],
                                                   center_volume),
                                   name="CenterLabelMap")
 

From 6c9886f3d4868138ddac39c9f5130157c479d5ba Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Tue, 12 Apr 2016 16:14:35 -0500
Subject: [PATCH 56/72] FIX: Replaces nipype.IdentityInterface with
 niu.IdentityInterface.

---
 nipype/workflows/smri/freesurfer/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index c9a530eb4b..9e88bbf389 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -602,7 +602,7 @@ def create_recoding_wf(in_file, out_file=None):
 
     wf.connect([(recode, center_labelmap, [('out_file', 'in_file')])])
 
-    outputspec = pe.Node(nipype.IdentityInterface(['recodedlabelmap']), name="outputspec")
+    outputspec = pe.Node(niu.IdentityInterface(['recodedlabelmap']), name="outputspec")
 
     wf.connect([(center_labelmap, outputspec, [('out_file', 'recodedlabelmap')])])
     return wf

From 01b84a9914768b3e9b96443bd743640f893b05b5 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 10:41:33 -0500
Subject: [PATCH 57/72] ENH: Removes the relabels hypointensities for 5.3.

---
 nipype/interfaces/freesurfer/utils.py         |  7 +++-
 .../workflows/smri/freesurfer/autorecon3.py   | 41 +++++++++----------
 2 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 8ef75478f1..d8a9379bd2 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2839,7 +2839,12 @@ def run(self, **inputs):
     def _format_arg(self, name, spec, value):
         if name == 'aseg':
             # aseg does not take a full filename
-            return spec.argstr % os.path.basename(value).replace('.mgz', '')
+            basename = os.path.basename(value).replace('.mgz', '')
+            if basename != 'aseg':
+                return spec.argstr % basename
+            else:
+                # aseg.mgz is the default
+                return
         elif name == 'out_file':
             return spec.argstr % os.path.abspath(value)
 
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index ad1cff1498..359f311f2b 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -550,14 +550,6 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
         #End hemisphere2 workflow
 
 
-    # Relabel Hypointensities
-    relabel_hypos = pe.Node(RelabelHypointensities(), name="Relabel_Hypointensities")
-    relabel_hypos.inputs.out_file = 'aseg.presurf.hypos.mgz'
-    ar3_wf.connect([(inputspec, relabel_hypos, [('aseg_presurf', 'aseg'),
-                                                ('lh_white', 'lh_white'),
-                                                ('rh_white', 'rh_white'),
-                                                ])])
-
     # APARC to ASEG
     # Adds information from the ribbon into the aseg.mgz (volume parcellation).
     aparc_2_aseg = pe.Node(Aparc2Aseg(), name="Aparc2Aseg")
@@ -578,9 +570,17 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (volume_mask, aparc_2_aseg, [('rh_ribbon', 'rh_ribbon'),
                                                  ('lh_ribbon', 'lh_ribbon'),
                                                  ('out_ribbon', 'ribbon'),
-                                                 ]),
-                    (relabel_hypos, aparc_2_aseg, [('out_file', 'aseg')])
-                    ])
+                                                 ])])
+    if fsvernum < 6:
+        ar3_wf.connect([(inputspec, aparc_2_aseg, [('aseg_presurf', 'aseg')])])
+    else:
+        # Relabel Hypointensities
+        relabel_hypos = pe.Node(RelabelHypointensities(), name="Relabel_Hypointensities")
+        relabel_hypos.inputs.out_file = 'aseg.presurf.hypos.mgz'
+        ar3_wf.connect([(inputspec, relabel_hypos, [('aseg_presurf', 'aseg'),
+                                                    ('lh_white', 'lh_white'),
+                                                    ('rh_white', 'rh_white')])])
+        ar3_wf.connect([(relabel_hypos, aparc_2_aseg, [('out_file', 'aseg')])])
 
     aparc_2_aseg_2009 = pe.Node(Aparc2Aseg(), name="Aparc2Aseg_2009")
     aparc_2_aseg_2009.inputs.volmask = True
@@ -601,14 +601,12 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (volume_mask, aparc_2_aseg_2009, [('rh_ribbon', 'rh_ribbon'),
                                                       ('lh_ribbon',
                                                        'lh_ribbon'),
-                                                      ('out_ribbon', 'ribbon'),
-                                                      ]),
-                    (relabel_hypos, aparc_2_aseg_2009, [('out_file', 'aseg')])
-                    ])
+                                                      ('out_ribbon', 'ribbon')])])
 
     if fsvernum > 6:
         apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
-        ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')])])        
+        ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')]),
+                        (relabel_hypos, aparc_2_aseg_2009, [('out_file', 'aseg')])])
     else:
         # aseg.mgz gets edited in place, so we'll copy and pass it to the
         # outputspec once aparc_2_aseg has completed
@@ -702,8 +700,7 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                                     ('out_ribbon', 'ribbon'),
                                                     ]),
                     (apas_2_aseg, wm_parcellation, [('out_file', 'aseg')]),
-                    (aparc_2_aseg, wm_parcellation, [('out_file', 'ctxseg')])
-                    ])
+                    (aparc_2_aseg, wm_parcellation, [('out_file', 'ctxseg')])])
 
     if fsvernum < 6:
         ar3_wf.connect([(inputspec, wm_parcellation, [('filled', 'filled')])])
@@ -745,7 +742,6 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
         ar3_wf.connect(inputspec, 'aseg_presurf', wm_segstats, 'aseg')
 
 
-
     # add brodman area maps to the workflow
     ba_WF, ba_outputs = create_ba_maps_wf(th3=th3, exvivo=exvivo,
                                           entorhinal=entorhinal)
@@ -937,11 +933,12 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                     (segstats, outputspec, [('summary_file', 'aseg_stats')]),
                     (aparc_2_aseg_2009, outputspec, [('out_file', 'aparc_a2009s_aseg')]),
                     (aparc_2_aseg, outputspec, [('out_file', 'aparc_aseg')]),
-                    (relabel_hypos, outputspec, [('out_file', 'aseg_presurf_hypos')]),
                     (volume_mask, outputspec, [('out_ribbon', 'ribbon'),
                                                ('lh_ribbon', 'lh_ribbon'),
-                                               ('rh_ribbon', 'rh_ribbon')]),
-                ])
+                                               ('rh_ribbon', 'rh_ribbon')])])
+    if fsvernum < 6:
+        ar3_wf.connect([(relabel_hypos, outputspec, [('out_file', 'aseg_presurf_hypos')])])
+
 
     for i, outputs in enumerate([hemi_outputs1, hemi_outputs2]):
         if i == 0:

From 89e208c91c618894251fc86494372f305b1969fe Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 10:45:43 -0500
Subject: [PATCH 58/72] FIX: Switches the presurf labelmap name back to
 aseg.presurf.mgz.

---
 nipype/workflows/smri/freesurfer/autorecon2.py | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index c616114fab..70459edf53 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -248,10 +248,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
                                ['out_file'],
                                copy_file),
                       name='Copy_CCSegmentation')
-    if fsvernum > 6:
-        copy_cc.inputs.out_file = 'aseg.presurf.mgz'
-    else:
-        copy_cc.inputs.out_file = 'aseg.mgz'
+    copy_cc.inputs.out_file = 'aseg.presurf.mgz'
 
     ar2_wf.connect([(segment_cc, copy_cc, [('out_file', 'in_file')])
                     ])

From aaf3b050b60f420fef6f7fca28671db68b3a44b7 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 10:58:48 -0500
Subject: [PATCH 59/72] FIX: make check-before-commit

---
 .../interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py   | 1 +
 nipype/interfaces/freesurfer/tests/test_auto_Curvature.py | 1 +
 .../interfaces/freesurfer/tests/test_auto_MakeSurfaces.py | 3 +++
 .../freesurfer/tests/test_auto_SegStatsReconAll.py        | 4 ++--
 .../interfaces/freesurfer/tests/test_auto_VolumeMask.py   | 3 +++
 nipype/interfaces/freesurfer/utils.py                     | 8 ++++----
 nipype/workflows/smri/freesurfer/autorecon1.py            | 8 ++++----
 nipype/workflows/smri/freesurfer/autorecon2.py            | 8 ++++----
 nipype/workflows/smri/freesurfer/autorecon3.py            | 4 ++--
 nipype/workflows/smri/freesurfer/ba_maps.py               | 2 +-
 nipype/workflows/smri/freesurfer/recon.py                 | 6 +++---
 11 files changed, 28 insertions(+), 20 deletions(-)

diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py
index 27ea0eb162..8925054f05 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py
@@ -19,6 +19,7 @@ def test_Aparc2Aseg_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    filled=dict(),
     hypo_wm=dict(argstr='--hypo-as-wm',
     mandatory=False,
     ),
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py
index 5be32abc21..851c2acff9 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py
@@ -19,6 +19,7 @@ def test_Curvature_inputs():
     usedefault=True,
     ),
     in_file=dict(argstr='%s',
+    copyfile=True,
     mandatory=True,
     position=-2,
     ),
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py
index f2ca8c2a64..a34894fe99 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py
@@ -35,6 +35,7 @@ def test_MakeSurfaces_inputs():
     in_orig=dict(argstr='-orig %s',
     mandatory=True,
     ),
+    in_white=dict(),
     in_wm=dict(mandatory=True,
     ),
     longitudinal=dict(argstr='-long',
@@ -66,6 +67,8 @@ def test_MakeSurfaces_inputs():
     subjects_dir=dict(),
     terminal_output=dict(nohash=True,
     ),
+    white=dict(argstr='-white %s',
+    ),
     white_only=dict(argstr='-whiteonly',
     mandatory=False,
     ),
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py
index e15967ffec..4c0f8dcde6 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py
@@ -10,6 +10,7 @@ def test_SegStatsReconAll_inputs():
     ),
     args=dict(argstr='%s',
     ),
+    aseg=dict(),
     avgwf_file=dict(argstr='--avgwfvol %s',
     ),
     avgwf_txt_file=dict(argstr='--avgwf %s',
@@ -85,8 +86,7 @@ def test_SegStatsReconAll_inputs():
     ),
     partial_volume_file=dict(argstr='--pv %s',
     ),
-    presurf_seg=dict(mandatory=True,
-    ),
+    presurf_seg=dict(),
     rh_orig_nofix=dict(mandatory=True,
     ),
     rh_pial=dict(mandatory=True,
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py
index 81786550f5..c87f8716b5 100644
--- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py
+++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py
@@ -6,6 +6,8 @@
 def test_VolumeMask_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    aseg=dict(xor=['in_aseg'],
+    ),
     copy_inputs=dict(mandatory=False,
     ),
     environ=dict(nohash=True,
@@ -16,6 +18,7 @@ def test_VolumeMask_inputs():
     ),
     in_aseg=dict(argstr='--aseg_name %s',
     mandatory=False,
+    xor=['aseg'],
     ),
     left_ribbonlabel=dict(argstr='--label_left_ribbon %d',
     mandatory=True,
diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index d8a9379bd2..975dda9975 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2315,14 +2315,14 @@ class VolumeMaskInputSpec(FSTraitedSpec):
     rh_white = File(mandatory=True, exists=True,
                     desc="Implicit input right white matter surface")
     aseg = File(exists=True,
-                xor=['in_aseg'], 
-                desc="Implicit aseg.mgz segmentation. " + 
+                xor=['in_aseg'],
+                desc="Implicit aseg.mgz segmentation. " +
                 "Specify a different aseg by using the 'in_aseg' input.")
     subject_id = traits.String('subject_id', usedefault=True,
                                position=-1, argstr="%s", mandatory=True,
                                desc="Subject being processed")
     # optional
-    in_aseg = File(argstr="--aseg_name %s", mandatory=False, 
+    in_aseg = File(argstr="--aseg_name %s", mandatory=False,
                    exists=True, xor=['aseg'],
                    desc="Input aseg file for VolumeMask")
     save_ribbon = traits.Bool(argstr="--save_ribbon", mandatory=False,
@@ -2383,7 +2383,7 @@ def run(self, **inputs):
             copy2subjdir(self, self.inputs.rh_white, 'surf', 'rh.white')
             copy2subjdir(self, self.inputs.in_aseg, 'mri')
             copy2subjdir(self, self.inputs.aseg, 'mri', 'aseg.mgz')
-            
+
         return super(VolumeMask, self).run(**inputs)
 
     def _format_arg(self, name, spec, value):
diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index d43121077f..161a690a9f 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -345,7 +345,7 @@ def awkfile(in_file, log_file):
         intensity_correction.inputs.iterations = 2
         ar1_wf.connect([(add_xform_to_orig, intensity_correction, [('out_file', 'in_file')]),
                         (copy_transform, intensity_correction, [('out_file', 'transform')])])
-        
+
 
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
         add_to_header_nu.inputs.copy_name = True
@@ -356,7 +356,7 @@ def awkfile(in_file, log_file):
                          [('out_file', 'transform')])
                     ])
 
-        
+
     # Intensity Normalization
     # Performs intensity normalization of the orig volume and places the result in mri/T1.mgz.
     # Attempts to correct for fluctuations in intensity that would otherwise make intensity-based
@@ -368,7 +368,7 @@ def awkfile(in_file, log_file):
     mri_normalize.inputs.out_file = 'T1.mgz'
 
     if fsvernum < 6:
-        ar1_wf.connect([(add_to_header_nu, mri_normalize, [('out_file', 'in_file')])])        
+        ar1_wf.connect([(add_to_header_nu, mri_normalize, [('out_file', 'in_file')])])
     else:
         ar1_wf.connect([(add_xform_to_orig_nu, mri_normalize, [('out_file', 'in_file')])])
 
@@ -390,7 +390,7 @@ def awkfile(in_file, log_file):
             ar1_wf.connect(add_to_header_nu, 'out_file', mri_em_register, 'in_file')
         else:
             ar1_wf.connect(add_xform_to_orig_nu, 'out_file', mri_em_register, 'in_file')
-            
+
         ar1_wf.connect([(inputspec, mri_em_register, [('num_threads', 'num_threads'),
                                                       ('reg_template_withskull', 'template')])])
 
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 70459edf53..3deabe6797 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -61,7 +61,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         ar2_wf.connect([(inputspec, intensity_correction, [('orig', 'in_file'),
                                                            ('brainmask', 'mask'),
                                                            ('transform', 'transform')])])
-        
+
         # intensity correction parameters are more specific in 6+
         intensity_correction.inputs.iterations = 1
         intensity_correction.inputs.protocol_iterations = 1000
@@ -70,7 +70,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         if shrink:
             intensity_correction.inputs.shrink =  shrink
         intensity_correction.inputs.distance = distance
-        
+
         add_to_header_nu = pe.Node(AddXFormToHeader(), name="Add_XForm_to_NU")
         add_to_header_nu.inputs.copy_name = True
         add_to_header_nu.inputs.out_file = 'nu.mgz'
@@ -108,7 +108,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
             ar2_wf.connect([(add_to_header_nu, align_transform, [('out_file', 'in_file')])])
         else:
             ar2_wf.connect([(inputspec, align_transform, [('nu', 'in_file')])])
-            
+
 
     # CA Normalize
     """
@@ -698,7 +698,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         # add to outputspec to perserve datasinking
         ar2_wf.connect([(inputspec, outputspec, [('nu', 'nu')])])
 
-    
+
     ar2_wf.connect([(align_transform, outputspec, [('out_file', 'tal_lta')]),
                     (ca_normalize, outputspec, [('out_file', 'norm')]),
                     (ca_normalize, outputspec, [('control_points', 'ctrl_pts')]),
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 359f311f2b..a4d5c5013c 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -621,10 +621,10 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                        out_aseg),
                               name="Aseg")
         ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_aparcaseg')]),
-                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])       
+                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])
 
     apas_2_aseg.inputs.out_file = "aseg.mgz"
-                                       
+
 
     # Segmentation Stats
     """
diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 34c978c102..2e10c61e9e 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -85,7 +85,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
                         out_file = '{0}.{1}_exvivo.label'.format(hemisphere, label)
                     else:
                         out_file = '{0}.{1}.label'.format(hemisphere, label)
-                        
+
                     out_files.append(out_file)
                     field_template[label] = 'label/' + out_file
                     source_fields.append(label)
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index f6996b6f2a..a4350ae425 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -167,7 +167,7 @@ def create_reconall_workflow(name="ReconAll", plugin_args=None,
         rb_date = "2008-03-26"
 
     print("FreeSurfer Version: {0}".format(fs_version))
-        
+
     def setconfig(reg_template=None,
                   reg_template_withskull=None,
                   lh_atlas=None,
@@ -234,14 +234,14 @@ def checkarg(arg, default):
               'lookup_table',
               'wm_lookup_table',
               'awk_file']
-    
+
     config_node = pe.Node(niu.Function(params + ['rb_date'],
                                        params,
                                        setconfig),
                           name="config")
 
     config_node.inputs.rb_date = rb_date
-    
+
     for param in params:
         reconall.connect(inputspec, param, config_node, param)
 

From 959c57e71984b6d02e59054e76a23520db34fd03 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 11:05:07 -0500
Subject: [PATCH 60/72] FIX: switches incorrect if statement.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index a4d5c5013c..04ab778609 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -936,7 +936,7 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                     (volume_mask, outputspec, [('out_ribbon', 'ribbon'),
                                                ('lh_ribbon', 'lh_ribbon'),
                                                ('rh_ribbon', 'rh_ribbon')])])
-    if fsvernum < 6:
+    if fsvernum > 6:
         ar3_wf.connect([(relabel_hypos, outputspec, [('out_file', 'aseg_presurf_hypos')])])
 
 

From 56fbd21b250d15be361106fc0b469fe105031ae7 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 15:02:52 -0500
Subject: [PATCH 61/72] FIX: Fixes aseg input for Aparc2Aseg.

---
 nipype/interfaces/freesurfer/utils.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py
index 975dda9975..6f03a11f6e 100644
--- a/nipype/interfaces/freesurfer/utils.py
+++ b/nipype/interfaces/freesurfer/utils.py
@@ -2840,11 +2840,7 @@ def _format_arg(self, name, spec, value):
         if name == 'aseg':
             # aseg does not take a full filename
             basename = os.path.basename(value).replace('.mgz', '')
-            if basename != 'aseg':
-                return spec.argstr % basename
-            else:
-                # aseg.mgz is the default
-                return
+            return spec.argstr % basename
         elif name == 'out_file':
             return spec.argstr % os.path.abspath(value)
 

From 3cd2fd0cfbed921453296fa6edf164f1f95b07fb Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 15:39:36 -0500
Subject: [PATCH 62/72] FIX: Adds aseg input for a2009s Aparc2Aseg.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 04ab778609..1c49e56bd0 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -621,7 +621,8 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                        out_aseg),
                               name="Aseg")
         ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_aparcaseg')]),
-                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')])])
+                        (inputspec, apas_2_aseg, [('aseg_presurf', 'in_aseg')]),
+                        (inputspec, aparc_2_aseg_2009, [('aseg_presurf', 'aseg')])])
 
     apas_2_aseg.inputs.out_file = "aseg.mgz"
 

From 5644aa2b268f51a6eac5a935d0f40af6b6153107 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 16:28:42 -0500
Subject: [PATCH 63/72] FIX: Adds stop and shrink values to autorecon2.py to
 ensure that the 6.0beta still works.

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 2 +-
 nipype/workflows/smri/freesurfer/autorecon2.py | 3 ++-
 nipype/workflows/smri/freesurfer/recon.py      | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index 161a690a9f..008563a737 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -36,7 +36,7 @@ def checkT1s(T1_files, cw256=False):
     return T1_files, cw256, resample_type, origvol_names
 
 def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
-                      custom_atlas=None, plugin_args=None, shrink=2, stop=0.0001,
+                      custom_atlas=None, plugin_args=None, shrink=None, stop=None,
                       fsvernum=5.3):
     """Creates the AutoRecon1 workflow in nipype.
 
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 3deabe6797..d3ff891af8 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -11,7 +11,8 @@ def copy_ltas(in_file, subjects_dir, subject_id, long_template):
     return out_file
 
 def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
-                      plugin_args=None, fsvernum=5.3):
+                      plugin_args=None, fsvernum=5.3,
+                          stop=None, shrink=None):
     # AutoRecon2
     # Workflow
     ar2_wf = pe.Workflow(name=name)
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index a4350ae425..2943e7e800 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -259,7 +259,8 @@ def checkarg(arg, default):
                                               'inputspec.reg_template_withskull'),
                                              ('awk_file', 'inputspec.awk_file')])])
     # create AutoRecon2
-    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum)
+    ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum,
+                                            stop=stop, shrink=shrink)
     # connect inputs for AutoRecon2
     reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads')]),
                       (config_node, ar2_wf, [('reg_template_withskull',

From 095e3592def74332606b9b571037429a2fcf6a41 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Wed, 13 Apr 2016 16:40:01 -0500
Subject: [PATCH 64/72] FIX: Adds distance to autorecon2.py.

---
 nipype/workflows/smri/freesurfer/autorecon1.py | 2 +-
 nipype/workflows/smri/freesurfer/autorecon2.py | 2 +-
 nipype/workflows/smri/freesurfer/recon.py      | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index 008563a737..0e11ab628c 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -35,7 +35,7 @@ def checkT1s(T1_files, cw256=False):
     resample_type = 'cubic' if len(T1_files) > 1 else 'interpolate'
     return T1_files, cw256, resample_type, origvol_names
 
-def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=200,
+def create_AutoRecon1(name="AutoRecon1", longitudinal=False, distance=None,
                       custom_atlas=None, plugin_args=None, shrink=None, stop=None,
                       fsvernum=5.3):
     """Creates the AutoRecon1 workflow in nipype.
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index d3ff891af8..053bb2a9a2 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -12,7 +12,7 @@ def copy_ltas(in_file, subjects_dir, subject_id, long_template):
 
 def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
                       plugin_args=None, fsvernum=5.3,
-                          stop=None, shrink=None):
+                      stop=None, shrink=None, distance=None):
     # AutoRecon2
     # Workflow
     ar2_wf = pe.Workflow(name=name)
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index 2943e7e800..9890380f94 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -260,7 +260,7 @@ def checkarg(arg, default):
                                              ('awk_file', 'inputspec.awk_file')])])
     # create AutoRecon2
     ar2_wf, ar2_outputs = create_AutoRecon2(plugin_args=plugin_args, fsvernum=fsvernum,
-                                            stop=stop, shrink=shrink)
+                                            stop=stop, shrink=shrink, distance=distance)
     # connect inputs for AutoRecon2
     reconall.connect([(inputspec, ar2_wf, [('num_threads', 'inputspec.num_threads')]),
                       (config_node, ar2_wf, [('reg_template_withskull',

From 3f1926ca1433344226fe6e760bc0778da8639fb6 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Thu, 14 Apr 2016 16:13:16 -0500
Subject: [PATCH 65/72] FIX: Corrected fsvernum if statements to fix 6.0beta
 workflow.

---
 nipype/workflows/smri/freesurfer/autorecon2.py |  2 +-
 nipype/workflows/smri/freesurfer/autorecon3.py | 14 +++++---------
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 053bb2a9a2..1e8ada6967 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -219,7 +219,7 @@ def create_AutoRecon2(name="AutoRecon2", longitudinal=False,
         fuse_segmentations.inputs.out_file = 'aseg.fused.mgz'
 
     ca_label = pe.Node(CALabel(), name='CA_Label')
-    if fsvernum > 6:
+    if fsvernum >= 6:
         ca_label.inputs.relabel_unlikely = (9, .3)
         ca_label.inputs.prior = 0.5
     ca_label.inputs.align = True
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 1c49e56bd0..5e74bc4103 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -286,7 +286,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                     (ar3_rh_wf1, volume_mask, [('outputspec.pial', 'rh_pial')]),
                     ])
 
-    if fsvernum > 6:
+    if fsvernum >= 6:
         ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'in_aseg')])])
     else:
         ar3_wf.connect([(inputspec, volume_mask, [('aseg_presurf', 'aseg')])])
@@ -296,12 +296,8 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
 
     for hemisphere, hemiwf2 in [('lh', ar3_lh_wf2),  ('rh', ar3_rh_wf2)]:
         if hemisphere == 'lh':
-            opp_hemi = 'rh'
-            opp_wf = ar3_rh_wf2
             hemiwf1 = ar3_lh_wf1
         else:
-            opp_hemi = 'lh'
-            opp_wf = ar3_lh_wf2
             hemiwf1 = ar3_rh_wf1
 
         hemi_inputs2 = ['wm',
@@ -603,7 +599,7 @@ def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
                                                        'lh_ribbon'),
                                                       ('out_ribbon', 'ribbon')])])
 
-    if fsvernum > 6:
+    if fsvernum >= 6:
         apas_2_aseg = pe.Node(Apas2Aseg(), name="Apas_2_Aseg")
         ar3_wf.connect([(aparc_2_aseg, apas_2_aseg, [('out_file', 'in_file')]),
                         (relabel_hypos, aparc_2_aseg_2009, [('out_file', 'aseg')])])
@@ -667,7 +663,7 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                            ]),
                     ])
 
-    if fsvernum > 6:
+    if fsvernum >= 6:
         ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'presurf_seg')
     else:
         ar3_wf.connect(inputspec, 'aseg_presurf', segstats, 'aseg')
@@ -737,7 +733,7 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                                               ]),
                     ])
 
-    if fsvernum > 6:
+    if fsvernum >= 6:
         ar3_wf.connect(inputspec, 'aseg_presurf', wm_segstats, 'presurf_seg')
     else:
         ar3_wf.connect(inputspec, 'aseg_presurf', wm_segstats, 'aseg')
@@ -937,7 +933,7 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
                     (volume_mask, outputspec, [('out_ribbon', 'ribbon'),
                                                ('lh_ribbon', 'lh_ribbon'),
                                                ('rh_ribbon', 'rh_ribbon')])])
-    if fsvernum > 6:
+    if fsvernum >= 6:
         ar3_wf.connect([(relabel_hypos, outputspec, [('out_file', 'aseg_presurf_hypos')])])
 
 

From f88204e6af6b0f83e91ac4e4b5c5c7fbcec13b78 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Thu, 14 Apr 2016 16:36:27 -0500
Subject: [PATCH 66/72] FIX: Removes duplicate connection.

---
 nipype/workflows/smri/freesurfer/autorecon3.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index 5e74bc4103..ea315ecfad 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -715,7 +715,6 @@ def out_aseg(in_aparcaseg, in_aseg, out_file):
     ar3_wf.connect([(wm_parcellation, wm_segstats, [('out_file', 'segmentation_file')]),
                     (inputspec, wm_segstats, [('lh_white', 'lh_white'),
                                               ('rh_white', 'rh_white'),
-                                              ('aseg_presurf', 'presurf_seg'),
                                               ('transform', 'transform'),
                                               ('norm', 'in_intensity'),
                                               ('norm', 'partial_volume_file'),

From 58cfc19be098e698ef5857e28f0a8c00e3c316ff Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 15 Apr 2016 09:27:24 -0500
Subject: [PATCH 67/72] FIX: Changes list position of entorhinal.

---
 nipype/workflows/smri/freesurfer/ba_maps.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/workflows/smri/freesurfer/ba_maps.py b/nipype/workflows/smri/freesurfer/ba_maps.py
index 2e10c61e9e..7fa266250c 100644
--- a/nipype/workflows/smri/freesurfer/ba_maps.py
+++ b/nipype/workflows/smri/freesurfer/ba_maps.py
@@ -58,7 +58,7 @@ def create_ba_maps_wf(name="Brodmann_Area_Maps", th3=True, exvivo=True,
     labels = ["BA1", "BA2", "BA3a", "BA3b", "BA4a", "BA4p", "BA6",
               "BA44", "BA45", "V1", "V2", "MT", "perirhinal"]
     if entorhinal:
-        labels.append('entorhinal')
+        labels.insert(-1, 'entorhinal')
     for hemisphere in ['lh', 'rh']:
         for threshold in [True, False]:
             field_template = dict(sphere_reg='surf/{0}.sphere.reg'.format(hemisphere),

From 816f787e8c6cc57bc29baf43e7c379d5e19c7ac3 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 15 Apr 2016 11:10:03 -0500
Subject: [PATCH 68/72] DOC: Updates CHANGES

---
 CHANGES | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGES b/CHANGES
index 337ae51f42..27c7ae31b7 100644
--- a/CHANGES
+++ b/CHANGES
@@ -28,6 +28,7 @@ Next release
 * FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
 * ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
 * FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
+* ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
 
 Release 0.11.0 (September 15, 2015)
 ============

From 6437bf31405bda1d19eb40bb97eb2e8e3521218b Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 15 Apr 2016 15:03:22 -0500
Subject: [PATCH 69/72] FIX: Removes unnecessary methods from smri freesurfer
 workflow utils.

---
 .../smri/freesurfer/recode_tables/fs2abc.csv  |  41 ----
 nipype/workflows/smri/freesurfer/recon.py     |  12 +-
 nipype/workflows/smri/freesurfer/utils.py     | 209 ------------------
 3 files changed, 1 insertion(+), 261 deletions(-)
 delete mode 100644 nipype/workflows/smri/freesurfer/recode_tables/fs2abc.csv

diff --git a/nipype/workflows/smri/freesurfer/recode_tables/fs2abc.csv b/nipype/workflows/smri/freesurfer/recode_tables/fs2abc.csv
deleted file mode 100644
index 76035d3b51..0000000000
--- a/nipype/workflows/smri/freesurfer/recode_tables/fs2abc.csv
+++ /dev/null
@@ -1,41 +0,0 @@
-orig_label,target_label
-41,1
-2,1
-42,2
-3,2
-77,2
-251,2
-252,2
-253,2
-254,2
-255,2
-43,4
-44,4
-4,4
-5,4
-14,4
-15,4
-24,4
-58,21
-50,21
-51,21
-52,21
-26,21
-11,21
-12,21
-13,21
-49,24
-60,24
-28,24
-10,24
-63,25
-53,25
-54,25
-31,25
-17,25
-18,25
-47,11
-8,11
-46,12
-7,12
-16,30
diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py
index b574314f35..0f1aad8913 100644
--- a/nipype/workflows/smri/freesurfer/recon.py
+++ b/nipype/workflows/smri/freesurfer/recon.py
@@ -79,8 +79,7 @@ def link_masks(subjects_dir, subject_id):
     wf.connect(autorecon_resume, "subject_id", outputnode, "subject_id")
     return wf
 
-def create_reconall_workflow(name="ReconAll", plugin_args=None,
-                             recoding_file=None):
+def create_reconall_workflow(name="ReconAll", plugin_args=None):
     """Creates the ReconAll workflow in nipype.
 
     Example
@@ -510,15 +509,6 @@ def completemethod(datasinked_files, subject_id):
                       (inputspec, completion, [('subject_id', 'subject_id')]),
                       (completion, postds_outputspec, [('subject_id', 'subject_id')])])
 
-
-    #### Workflow additions go here
-    if recoding_file:
-        from utils import create_recoding_wf
-        recode = create_recoding_wf(recoding_file)
-        reconall.connect([(ar3_wf, recode, [('outputspec.aseg', 'inputspec.labelmap')]),
-                          (recode, outputspec, [('outputspec.recodedlabelmap', 'recoded_labelmap')])])
-
-
     return reconall
 
 
diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 7ce98a4642..023cf612ec 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -493,79 +493,6 @@ def checkenv(exitonfail=False):
     else:
         print("Warning: " + msg)
 
-def center_volume(in_file):
-    import SimpleITK as sitk
-    import os
-    img = sitk.ReadImage(in_file)
-    size = img.GetSize()
-    origin = img.GetOrigin()
-    new_origin = [0,0,0]
-    for i, xx in enumerate(origin):
-        new_origin[i] = float(size[i])/2
-        if xx < 0:
-            new_origin[i] = -new_origin[i]
-    img.SetOrigin(new_origin)
-    out_file = os.path.abspath(os.path.basename(in_file))
-    sitk.WriteImage(img, out_file)
-    return out_file
-
-
-def recodeLabelMap(in_file, out_file, recode_file):
-    """This function has been adapted from BRAINSTools and serves
-    as a means to recode a label map based upon an input csv
-    file."""
-    import SimpleITK as sitk
-    import os
-    import csv
-    import sys
-
-    # Convert csv to RECODE_TABLE
-    CSVFile = open(recode_file, 'rb')
-    reader = csv.reader(CSVFile)
-    header = reader.next()
-    n_cols = len(header)
-    if n_cols == 4:
-        # ignore label names
-        label_keys = (0, 2)
-    elif n_cols == 2:
-        # no label names present
-        label_keys = (0, 1)
-    else:
-        # csv does not match format requirements
-        print("ERROR: input csv file for label recoding does meet requirements")
-        sys.exit()
-
-    # read csv file
-    RECODE_TABLE = list()
-    for line in reader:
-        RECODE_TABLE.append((int(line[label_keys[0]]), int(line[label_keys[1]])))
-
-    def minimizeSizeOfImage(outlabels):
-        """This function will find the largest integer value in the labelmap, and
-        cast the image to the smallest possible integer size so that no loss of data
-        results."""
-        measureFilt  = sitk.StatisticsImageFilter()
-        measureFilt.Execute(outlabels)
-        imgMin=measureFilt.GetMinimum()
-        imgMax=measureFilt.GetMaximum()
-        if imgMax < (2**8)-1:
-            outlabels = sitk.Cast( outlabels, sitk.sitkUInt8 )
-        elif imgMax < (2**16)-1:
-            outlabels = sitk.Cast( outlabels, sitk.sitkUInt16 )
-        elif imgMax < (2**32)-1:
-            outlabels = sitk.Cast( outlabels, sitk.sitkUInt32 )
-        elif imgMax < (2**64)-1:
-            outlabels = sitk.Cast( outlabels, sitk.sitkUInt64 )
-        return outlabels
-
-    LabelImage=sitk.Cast(sitk.ReadImage(in_file), sitk.sitkUInt32)
-    for (old, new) in RECODE_TABLE:
-        LabelImage = sitk.Cast((LabelImage == old), sitk.sitkUInt32)*(new - old)+LabelImage
-    LabelImage = minimizeSizeOfImage(LabelImage)
-    out_file = os.path.abspath(out_file)
-    sitk.WriteImage(LabelImage, out_file)
-    return out_file
-
 
 def create_recoding_wf(in_file, out_file=None):
     wf = nipype.Workflow(name="RecodeLabels")
@@ -729,139 +656,3 @@ def createsrcsubj(source_directory):
         rh_entorhinal_exvivo_thresh='label/rh.entorhinal_exvivo.thresh.label',
         rh_perirhinal_exvivo_thresh='label/rh.perirhinal_exvivo.thresh.label')
     return datasource, outfields
-
-def source_long_files_workflow(name="Source_Longitudinal_Files"):
-    """Creates a workflow to source the longitudinal files from a freesurfer directory.
-    This should only be used when the files are not in a prexisting workflow"""
-
-    wf = Workflow(name=name)
-
-    inputspec = Node(IdentityInterface(fields=['subject_id',
-                                               'subjects_dir',
-                                               'timepoints']),
-                     name="inputspec")
-
-    # TODO: Create outputspec
-
-    # grab files from the initial single session run
-    grab_inittp_files = pe.Node(nio.DataGrabber(), name="Grab_Initial_Files",
-                                infields=['subject_id'],
-                                outfileds=['inputvols', 'iscales', 'ltas'])
-    grab_inittp_files.inputs.template = '*'
-    grab_inittp_files.inputs.base_directory = config['subjects_dir']
-    grab_inittp_files.inputs.field_template = dict(inputvols='%s/mri/orig/0*.mgz',
-                                                   iscales='%s/mri/orig/0*-iscale.txt',
-                                                   ltas='%s/mri/orig/0*.lta')
-
-    grab_inittp_files.inputs.template_args = dict(inputvols=[['subject_id']],
-                                                  iscales=[['subject_id']],
-                                                  ltas=[['subject_id']])
-
-    wf.connect([(grab_inittp_files, outputspec, [('inputvols', 'inputspec.in_T1s'),
-                                                   ('iscales', 'inputspec.iscales'),
-                                                   ('ltas', 'inputspec.ltas')])])
-
-    merge_norms = pe.Node(Merge(len(config['timepoints'])), name="Merge_Norms")
-    merge_segs = pe.Node(Merge(len(config['timepoints'])), name="Merge_Segmentations")
-    merge_segs_noCC = pe.Node(Merge(len(config['timepoints'])), name="Merge_Segmentations_noCC")
-    merge_template_ltas = pe.Node(Merge(len(config['timepoints'])), name="Merge_Template_ltas")
-
-    for i, tp in enumerate(config['timepoints']):
-        # datasource timepoint files
-        tp_data_source = pe.Node(FreeSurferSource(), name="{0}_DataSource".format(tp))
-        tp_data_source.inputs.subject_id = tp
-        tp_data_source.inputs.subjects_dir = config['subjects_dir']
-
-        tp_data_grabber = pe.Node(nio.DataGrabber(), name="{0}_DataGrabber".format(tp),
-                                  infields=['tp', 'long_tempate'],
-                                  outfileds=['subj_to_template_lta', 'seg_noCC', 'seg_presurf'])
-        tp_data_grabber.inputs.template = '*'
-        tp_data_grabber.inputs.base_directory = config['subjects_dir']
-        tp_data_grabber.inputs.field_template = dict(
-            subj_to_template_lta='%s/mri/transforms/%s_to_%s.lta',
-            seg_noCC='%s/mri/aseg.auto_noCCseg.mgz',
-            seg_presurf='%s/mri/aseg.presurf.mgz',)
-
-        tp_data_grabber.inputs.template_args = dict(
-            subj_to_template_lta=[['long_template', 'tp', 'long_template']],
-            seg_noCC=[['tp']],
-            seg_presurf=[['tp']])
-
-        wf.connect([(tp_data_source, merge_norms, [('norm',
-                                                          'in{0}'.format(i))]),
-                          (tp_data_grabber, merge_segs, [('seg_presurf',
-                                                          'in{0}'.format(i))]),
-                          (tp_data_grabber, merge_segs_noCC, [('seg_noCC',
-                                                               'in{0}'.format(i))]),
-                          (tp_data_grabber, merge_template_ltas, [('subj_to_template_lta',
-                                                                   'in{0}'.format(i))])])
-
-        if tp == config['subject_id']:
-            wf.connect([(tp_data_source, outputspec, [('wm', 'inputspec.init_wm')]),
-                              (tp_data_grabber, outputspec, [('subj_to_template_lta',
-                                                          'inputspec.subj_to_template_lta')]),
-                              (tp_data_grabber, outputspec, [('subj_to_template_lta',
-                                                          'inputspec.subj_to_template_lta')])])
-
-    wf.connect([(merge_norms, outputspec, [('out', 'inputspec.alltps_norms')]),
-                      (merge_segs, outputspec, [('out', 'inputspec.alltps_segs')]),
-                      (merge_template_ltas, outputspec, [('out', 'inputspec.alltps_to_template_ltas')]),
-                      (merge_segs_noCC, outputspec, [('out', 'inputspec.alltps_segs_noCC')])])
-
-
-
-    # datasource files from the template run
-    ds_template_files = pe.Node(FreeSurferSource(), name="Datasource_Template_Files")
-    ds_template_files.inputs.subject_id = config['subject_id']
-    ds_template_files.inputs.subjects_dir = config['subjects_dir']
-
-    wf.connect([(ds_template_files, ar1_wf, [('brainmask', 'inputspec.template_brainmask')]),
-                      (ds_template_files, outputspec, [('aseg', 'inputspec.template_aseg')])])
-
-    # grab files from template run
-    grab_template_files = pe.Node(nio.DataGrabber(), name="Grab_Template_Files",
-                                  infields=['subject_id', 'long_template'],
-                                  outfields=['template_talairach_xfm',
-                                             'template_talairach_lta',
-                                             'template_talairach_m3z',
-                                             'template_label_intensities',
-                                             'template_lh_white',
-                                             'template_rh_white',
-                                             'template_lh_pial',
-                                             'template_rh_pial'])
-    grab_template_files.inputs.template = '*'
-    grab_template_files.inputs.base_directory = config['subjects_dir']
-    grab_template_files.inputs.subject_id = config['subject_id']
-    grab_template_files.inputs.long_template = config['long_template']
-    grab_template_files.inputs.field_template = dict(
-        template_talairach_xfm='%s/mri/transfroms/talairach.xfm',
-        template_talairach_lta='%s/mri/transfroms/talairach.lta',
-        template_talairach_m3z='%s/mri/transfroms/talairach.m3z',
-        template_label_intensities='%s/mri/aseg.auto_noCCseg.label_intensities.txt',
-        template_lh_white='%s/surf/lh.white',
-        template_rh_white='%s/surf/rh.white',
-        template_lh_pial='%s/surf/lh.pial',
-        template_rh_pial='%s/surf/rh.pial')
-
-    grab_template_files.inputs.template_args = dict(
-        template_talairach_xfm=[['long_template']],
-        template_talairach_lta=[['long_template']],
-        template_talairach_m3z=[['long_template']],
-        template_lh_white=[['long_template']],
-        template_rh_white=[['long_template']],
-        template_lh_pial=[['long_template']],
-        template_rh_pial=[['long_template']])
-    wf.connect([(grab_template_files, outputspec, [('template_talairach_xfm',
-                                                    'inputspec.template_talairach_xfm'),
-                                                   ('template_talairach_lta',
-                                                    'inputspec.template_talairach_lta'),
-                                                   ('template_talairach_m3z',
-                                                    'inputspec.template_talairach_m3z'),
-                                                   ('template_label_intensities',
-                                                    'inputspec.template_label_intensities'),
-                                                   ('template_lh_white', 'inputspec.template_lh_white'),
-                                                   ('template_rh_white', 'inputspec.template_rh_white'),
-                                                   ('template_lh_pial', 'inputspec.template_lh_pial'),
-                                                   ('template_rh_pial', 'inputspec.template_rh_pial')])
-            ])
-    return wf

From c39acaf35ea58afc620e8b49b2768b1b25ceacc6 Mon Sep 17 00:00:00 2001
From: David Ellis <david-ellis@uiowa.edu>
Date: Fri, 15 Apr 2016 16:56:42 -0500
Subject: [PATCH 70/72] FIX: Removes unused functions and imports.

---
 .../workflows/smri/freesurfer/autorecon1.py   |   5 +-
 .../workflows/smri/freesurfer/autorecon2.py   |   2 -
 .../workflows/smri/freesurfer/autorecon3.py   |   5 +-
 nipype/workflows/smri/freesurfer/utils.py     | 164 ------------------
 4 files changed, 2 insertions(+), 174 deletions(-)

diff --git a/nipype/workflows/smri/freesurfer/autorecon1.py b/nipype/workflows/smri/freesurfer/autorecon1.py
index b77b65465c..e29a949166 100644
--- a/nipype/workflows/smri/freesurfer/autorecon1.py
+++ b/nipype/workflows/smri/freesurfer/autorecon1.py
@@ -1,10 +1,7 @@
-import sys
-import os
-import nipype
 from nipype.interfaces.utility import Function,IdentityInterface
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
-from .utils import copy_file, copy_files
+from .utils import copy_file
 
 
 def checkT1s(T1_files, cw256=False):
diff --git a/nipype/workflows/smri/freesurfer/autorecon2.py b/nipype/workflows/smri/freesurfer/autorecon2.py
index 2fd85bce13..f09e991439 100644
--- a/nipype/workflows/smri/freesurfer/autorecon2.py
+++ b/nipype/workflows/smri/freesurfer/autorecon2.py
@@ -1,5 +1,3 @@
-import os
-import nipype
 from nipype.interfaces.utility import Function, IdentityInterface, Merge
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
diff --git a/nipype/workflows/smri/freesurfer/autorecon3.py b/nipype/workflows/smri/freesurfer/autorecon3.py
index ffc0eec7b9..656f81188e 100644
--- a/nipype/workflows/smri/freesurfer/autorecon3.py
+++ b/nipype/workflows/smri/freesurfer/autorecon3.py
@@ -1,10 +1,7 @@
-import os
-import nipype
-from nipype.interfaces.utility import Function, IdentityInterface, Merge
+from nipype.interfaces.utility import IdentityInterface, Merge
 import nipype.pipeline.engine as pe  # pypeline engine
 from nipype.interfaces.freesurfer import *
 from .ba_maps import create_ba_maps_wf
-from .utils import createsrcsubj
 from nipype.interfaces.io import DataGrabber
 
 def create_AutoRecon3(name="AutoRecon3", qcache=False, plugin_args=None,
diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py
index 023cf612ec..74d45776d2 100644
--- a/nipype/workflows/smri/freesurfer/utils.py
+++ b/nipype/workflows/smri/freesurfer/utils.py
@@ -492,167 +492,3 @@ def checkenv(exitonfail=False):
         sys.exit(2)
     else:
         print("Warning: " + msg)
-
-
-def create_recoding_wf(in_file, out_file=None):
-    wf = nipype.Workflow(name="RecodeLabels")
-
-    inputspec = nipype.pipeline.Node(nipype.IdentityInterface(['labelmap',
-                                                               'recode_file']),
-                                     name="inputspec")
-    inputspec.inputs.recode_file = in_file
-
-    convert_labelmap = nipype.pipeline.Node(fs.MRIConvert(), name="ConvertLabelMap")
-    convert_labelmap.inputs.in_type = 'mgz'
-    convert_labelmap.inputs.out_type = 'nii'
-    convert_labelmap.inputs.out_orientation = 'RAS'
-    convert_labelmap.inputs.out_file = 'labelmap.nii'
-    wf.connect([(inputspec, convert_labelmap, [('labelmap', 'in_file')])])
-
-    recode = nipype.Node(nipype.Function(['in_file',
-                                          'out_file',
-                                          'recode_file'],
-                                         ['out_file'],
-                                         recodeLabelMap),
-                         name = "RecodeLabelMap")
-    if out_file == None:
-        recode.inputs.out_file = 'recodedlabelmap.nii'
-    else:
-        recode.inputs.out_file = out_file
-
-    wf.connect([(convert_labelmap, recode, [('out_file', 'in_file')]),
-                (inputspec, recode, [('recode_file', 'recode_file')])])
-
-    center_labelmap = nipype.Node(nipype.Function(['in_file'], ['out_file'],
-                                                  center_volume),
-                                  name="CenterLabelMap")
-
-    wf.connect([(recode, center_labelmap, [('out_file', 'in_file')])])
-
-    outputspec = nipype.Node(nipype.IdentityInterface(['recodedlabelmap']), name="outputspec")
-
-    wf.connect([(center_labelmap, outputspec, [('out_file', 'recodedlabelmap')])])
-    return wf
-
-def createsrcsubj(source_directory):
-    """
-    Returns a node that acts as the datasource for a source subject such as
-    'fsaverage'
-    """
-    outfields = ['lh_BA1_exvivo',
-                 'lh_BA2_exvivo',
-                 'lh_BA3a_exvivo',
-                 'lh_BA3b_exvivo',
-                 'lh_BA4a_exvivo',
-                 'lh_BA4p_exvivo',
-                 'lh_BA6_exvivo',
-                 'lh_BA44_exvivo',
-                 'lh_BA45_exvivo',
-                 'lh_V1_exvivo',
-                 'lh_V2_exvivo',
-                 'lh_MT_exvivo',
-                 'lh_entorhinal_exvivo',
-                 'lh_perirhinal_exvivo',
-                 'lh_BA1_exvivo_thresh',
-                 'lh_BA2_exvivo_thresh',
-                 'lh_BA3a_exvivo_thresh',
-                 'lh_BA3b_exvivo_thresh',
-                 'lh_BA4a_exvivo_thresh',
-                 'lh_BA4p_exvivo_thresh',
-                 'lh_BA6_exvivo_thresh',
-                 'lh_BA44_exvivo_thresh',
-                 'lh_BA45_exvivo_thresh',
-                 'lh_V1_exvivo_thresh',
-                 'lh_V2_exvivo_thresh',
-                 'lh_MT_exvivo_thresh',
-                 'lh_entorhinal_exvivo_thresh',
-                 'lh_perirhinal_exvivo_thresh',
-                 'rh_BA1_exvivo',
-                 'rh_BA2_exvivo',
-                 'rh_BA3a_exvivo',
-                 'rh_BA3b_exvivo',
-                 'rh_BA4a_exvivo',
-                 'rh_BA4p_exvivo',
-                 'rh_BA6_exvivo',
-                 'rh_BA44_exvivo',
-                 'rh_BA45_exvivo',
-                 'rh_V1_exvivo',
-                 'rh_V2_exvivo',
-                 'rh_MT_exvivo',
-                 'rh_entorhinal_exvivo',
-                 'rh_perirhinal_exvivo',
-                 'rh_BA1_exvivo_thresh',
-                 'rh_BA2_exvivo_thresh',
-                 'rh_BA3a_exvivo_thresh',
-                 'rh_BA3b_exvivo_thresh',
-                 'rh_BA4a_exvivo_thresh',
-                 'rh_BA4p_exvivo_thresh',
-                 'rh_BA6_exvivo_thresh',
-                 'rh_BA44_exvivo_thresh',
-                 'rh_BA45_exvivo_thresh',
-                 'rh_V1_exvivo_thresh',
-                 'rh_V2_exvivo_thresh',
-                 'rh_MT_exvivo_thresh',
-                 'rh_entorhinal_exvivo_thresh',
-                 'rh_perirhinal_exvivo_thresh']
-    datasource = pe.Node(nio.nio.DataGrabber(outfields=outfields), name="Source_Subject")
-    datasource.inputs.base_directory = source_directory
-    datasource.inputs.template = '*'
-    datasource.inputs.field_template = dict(
-        lh_BA1_exvivo='label/lh.BA1_exvivo.label',
-        lh_BA2_exvivo='label/lh.BA2_exvivo.label',
-        lh_BA3a_exvivo='label/lh.BA3a_exvivo.label',
-        lh_BA3b_exvivo='label/lh.BA3b_exvivo.label',
-        lh_BA4a_exvivo='label/lh.BA4a_exvivo.label',
-        lh_BA4p_exvivo='label/lh.BA4p_exvivo.label',
-        lh_BA6_exvivo='label/lh.BA6_exvivo.label',
-        lh_BA44_exvivo='label/lh.BA44_exvivo.label',
-        lh_BA45_exvivo='label/lh.BA45_exvivo.label',
-        lh_V1_exvivo='label/lh.V1_exvivo.label',
-        lh_V2_exvivo='label/lh.V2_exvivo.label',
-        lh_MT_exvivo='label/lh.MT_exvivo.label',
-        lh_entorhinal_exvivo='label/lh.entorhinal_exvivo.label',
-        lh_perirhinal_exvivo='label/lh.perirhinal_exvivo.label',
-        lh_BA1_exvivo_thresh='label/lh.BA1_exvivo.thresh.label',
-        lh_BA2_exvivo_thresh='label/lh.BA2_exvivo.thresh.label',
-        lh_BA3a_exvivo_thresh='label/lh.BA3a_exvivo.thresh.label',
-        lh_BA3b_exvivo_thresh='label/lh.BA3b_exvivo.thresh.label',
-        lh_BA4a_exvivo_thresh='label/lh.BA4a_exvivo.thresh.label',
-        lh_BA4p_exvivo_thresh='label/lh.BA4p_exvivo.thresh.label',
-        lh_BA6_exvivo_thresh='label/lh.BA6_exvivo.thresh.label',
-        lh_BA44_exvivo_thresh='label/lh.BA44_exvivo.thresh.label',
-        lh_BA45_exvivo_thresh='label/lh.BA45_exvivo.thresh.label',
-        lh_V1_exvivo_thresh='label/lh.V1_exvivo.thresh.label',
-        lh_V2_exvivo_thresh='label/lh.V2_exvivo.thresh.label',
-        lh_MT_exvivo_thresh='label/lh.MT_exvivo.thresh.label',
-        lh_entorhinal_exvivo_thresh='label/lh.entorhinal_exvivo.thresh.label',
-        lh_perirhinal_exvivo_thresh='label/lh.perirhinal_exvivo.thresh.label',
-        rh_BA1_exvivo='label/rh.BA1_exvivo.label',
-        rh_BA2_exvivo='label/rh.BA2_exvivo.label',
-        rh_BA3a_exvivo='label/rh.BA3a_exvivo.label',
-        rh_BA3b_exvivo='label/rh.BA3b_exvivo.label',
-        rh_BA4a_exvivo='label/rh.BA4a_exvivo.label',
-        rh_BA4p_exvivo='label/rh.BA4p_exvivo.label',
-        rh_BA6_exvivo='label/rh.BA6_exvivo.label',
-        rh_BA44_exvivo='label/rh.BA44_exvivo.label',
-        rh_BA45_exvivo='label/rh.BA45_exvivo.label',
-        rh_V1_exvivo='label/rh.V1_exvivo.label',
-        rh_V2_exvivo='label/rh.V2_exvivo.label',
-        rh_MT_exvivo='label/rh.MT_exvivo.label',
-        rh_entorhinal_exvivo='label/rh.entorhinal_exvivo.label',
-        rh_perirhinal_exvivo='label/rh.perirhinal_exvivo.label',
-        rh_BA1_exvivo_thresh='label/rh.BA1_exvivo.thresh.label',
-        rh_BA2_exvivo_thresh='label/rh.BA2_exvivo.thresh.label',
-        rh_BA3a_exvivo_thresh='label/rh.BA3a_exvivo.thresh.label',
-        rh_BA3b_exvivo_thresh='label/rh.BA3b_exvivo.thresh.label',
-        rh_BA4a_exvivo_thresh='label/rh.BA4a_exvivo.thresh.label',
-        rh_BA4p_exvivo_thresh='label/rh.BA4p_exvivo.thresh.label',
-        rh_BA6_exvivo_thresh='label/rh.BA6_exvivo.thresh.label',
-        rh_BA44_exvivo_thresh='label/rh.BA44_exvivo.thresh.label',
-        rh_BA45_exvivo_thresh='label/rh.BA45_exvivo.thresh.label',
-        rh_V1_exvivo_thresh='label/rh.V1_exvivo.thresh.label',
-        rh_V2_exvivo_thresh='label/rh.V2_exvivo.thresh.label',
-        rh_MT_exvivo_thresh='label/rh.MT_exvivo.thresh.label',
-        rh_entorhinal_exvivo_thresh='label/rh.entorhinal_exvivo.thresh.label',
-        rh_perirhinal_exvivo_thresh='label/rh.perirhinal_exvivo.thresh.label')
-    return datasource, outfields

From 461b17b639482518ba2e5d4eee3a7886226408fb Mon Sep 17 00:00:00 2001
From: Alexandre Manhaes Savio <alexsavio@gmail.com>
Date: Thu, 7 Apr 2016 14:05:45 +0200
Subject: [PATCH 71/72] add nipype_crash_search script

---
 bin/nipype_crash_search.py | 76 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100755 bin/nipype_crash_search.py

diff --git a/bin/nipype_crash_search.py b/bin/nipype_crash_search.py
new file mode 100755
index 0000000000..068e5d600a
--- /dev/null
+++ b/bin/nipype_crash_search.py
@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+"""Search for tracebacks inside a folder of nipype crash
+log files that match a given regular expression.
+
+Examples:
+nipype_crash_search -d nipype/wd/log -r '.*subject123.*'
+"""
+import re
+import os.path as op
+from glob import glob
+
+from traits.trait_errors import TraitError
+from nipype.utils.filemanip import loadcrash
+
+
+def load_pklz_traceback(crash_filepath):
+    """ Return the traceback message in the given crash file."""
+    try:
+        data = loadcrash(crash_filepath)
+    except TraitError as te:
+        return str(te)
+    except:
+        raise
+    else:
+        return '\n'.join(data['traceback'])
+
+
+def iter_tracebacks(logdir):
+    """ Return an iterator over each file path and
+    traceback field inside `logdir`.
+    Parameters
+    ----------
+    logdir: str
+        Path to the log folder.
+
+    field: str
+        Field name to be read from the crash file.
+
+    Yields
+    ------
+    path_file: str
+
+    traceback: str
+    """
+    crash_files = sorted(glob(op.join(logdir, '*.pkl*')))
+
+    for cf in crash_files:
+        yield cf, load_pklz_traceback(cf)
+
+
+def display_crash_search(logdir, regex):
+    rex = re.compile(regex, re.IGNORECASE)
+    for file, trace in iter_tracebacks(logdir):
+        if rex.search(trace):
+            print("-" * len(file))
+            print(file)
+            print("-" * len(file))
+            print(trace)
+
+
+if __name__ == "__main__":
+    from argparse import ArgumentParser, RawTextHelpFormatter
+    defstr = ' (default %(default)s)'
+    parser = ArgumentParser(prog='nipype_crash_search',
+                            description=__doc__,
+                            formatter_class=RawTextHelpFormatter)
+    parser.add_argument('-l','--logdir', type=str, dest='logdir',
+                        action="store", default=None,
+                        help='The working directory log file.' + defstr)
+    parser.add_argument('-r', '--regex', dest='regex',
+                        default='*',
+                        help='Regular expression to be searched in each traceback.' + defstr)
+
+    args = parser.parse_args()
+
+    display_crash_search(args.logdir, args.regex)

From d76723295fc3feb1887c09aa003bf2ce14ac2353 Mon Sep 17 00:00:00 2001
From: Alexandre Manhaes Savio <alexsavio@gmail.com>
Date: Mon, 18 Apr 2016 11:18:23 +0200
Subject: [PATCH 72/72] add doc for nipype_crash_search

---
 CHANGES             |   1 +
 CHANGES.orig        | 538 --------------------------------------------
 doc/users/debug.rst |   3 +
 3 files changed, 4 insertions(+), 538 deletions(-)
 delete mode 100644 CHANGES.orig

diff --git a/CHANGES b/CHANGES
index 27c7ae31b7..5c927ac77c 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,6 +1,7 @@
 Next release
 ============
 
+* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
 * ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
 * FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
 * FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
diff --git a/CHANGES.orig b/CHANGES.orig
deleted file mode 100644
index b7a849dd7e..0000000000
--- a/CHANGES.orig
+++ /dev/null
@@ -1,538 +0,0 @@
-Next release
-============
-
-* FIX: job execution on systems/approaches where locale is undefined (https://github.com/nipy/nipype/pull/1401)
-* FIX: Clean up byte/unicode issues using subprocess (https://github.com/nipy/nipype/pull/1394)
-* FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
-* ENH: New interfaces in dipy: RESTORE, EstimateResponseSH, CSD and StreamlineTractography
-       (https://github.com/nipy/nipype/pull/1090)
-* ENH: Added interfaces of AFNI (https://github.com/nipy/nipype/pull/1360,
-       https://github.com/nipy/nipype/pull/1361, https://github.com/nipy/nipype/pull/1382)
-* ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
-* ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
-* ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
-* TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
-* ENH: Add new flags to the BRAINSABC for new features (https://github.com/nipy/nipype/pull/1322)
-* ENH: Provides a Nipype wrapper for ANTs DenoiseImage (https://github.com/nipy/nipype/pull/1291)
-* FIX: Minor bugfix logging hash differences (https://github.com/nipy/nipype/pull/1298)
-* FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
-* ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
-* FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
-* ENH: Added an OAR scheduler plugin (https://github.com/nipy/nipype/pull/1259)
-* ENH: New ANTs interface: antsBrainExtraction (https://github.com/nipy/nipype/pull/1231)
-* API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
-* ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
-* ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
-* FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
-* FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
-* ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
-=======
-
-Release 0.11.0 (September 15, 2015)
-============
-
-* API: Change how hash values are computed (https://github.com/nipy/nipype/pull/1174)
-* ENH: New algorithm: mesh.WarpPoints applies displacements fields to point sets
-       (https://github.com/nipy/nipype/pull/889).
-* ENH: New interfaces for MRTrix3 (https://github.com/nipy/nipype/pull/1126)
-* ENH: New option in afni.3dRefit - zdel, ydel, zdel etc. (https://github.com/nipy/nipype/pull/1079)
-* FIX: ants.Registration composite transform outputs are no longer returned as lists (https://github.com/nipy/nipype/pull/1183)
-* BUG: ANTs Registration interface failed with multi-modal inputs
-    (https://github.com/nipy/nipype/pull/1176) (https://github.com/nipy/nipype/issues/1175)
-* ENH: dipy.TrackDensityMap interface now accepts a reference image (https://github.com/nipy/nipype/pull/1091)
-* FIX: Bug in XFibres5 (https://github.com/nipy/nipype/pull/1168)
-* ENH: Attempt to use hard links for data sink.
-    (https://github.com/nipy/nipype/pull/1161)
-* FIX: Updates to SGE Plugins
-    (https://github.com/nipy/nipype/pull/1129)
-* ENH: Add ants JointFusion() node with testing
-    (https://github.com/nipy/nipype/pull/1160)
-* ENH: Add --float option for antsRegistration calls
-    (https://github.com/nipy/nipype/pull/1159)
-* ENH: Added interface to simulate DWIs using the multi-tensor model
-       (https://github.com/nipy/nipype/pull/1085)
-* ENH: New interface for FSL fslcpgeom utility (https://github.com/nipy/nipype/pull/1152)
-* ENH: Added SLURMGraph plugin for submitting jobs to SLURM with dependencies (https://github.com/nipy/nipype/pull/1136)
-* FIX: Enable absolute path definitions in DCMStack (https://github.com/nipy/nipype/pull/1089,
-       replaced by https://github.com/nipy/nipype/pull/1093)
-* ENH: New mesh.MeshWarpMaths to operate on surface-defined warpings
-       (https://github.com/nipy/nipype/pull/1016)
-* FIX: Refactor P2PDistance, change name to ComputeMeshWarp, add regression tests,
-       fix bug in area weighted distance, and added optimizations
-       (https://github.com/nipy/nipype/pull/1016)
-* ENH: Add an option not to resubmit Nodes that finished running when using SGEGraph (https://github.com/nipy/nipype/pull/1002)
-* FIX: FUGUE is now properly listing outputs. (https://github.com/nipy/nipype/pull/978)
-* ENH: Improved FieldMap-Based (FMB) workflow for correction of susceptibility distortions in EPI seqs.
-       (https://github.com/nipy/nipype/pull/1019)
-* FIX: In the FSLXcommand _list_outputs function fixed for loop range (https://github.com/nipy/nipype/pull/1071)
-* ENH: Dropped support for now 7 years old Python 2.6 (https://github.com/nipy/nipype/pull/1069)
-* FIX: terminal_output is not mandatory anymore (https://github.com/nipy/nipype/pull/1070)
-* ENH: Added "nipype_cmd" tool for running interfaces from the command line (https://github.com/nipy/nipype/pull/795)
-* FIX: Fixed Camino output naming (https://github.com/nipy/nipype/pull/1061)
-* ENH: Add the average distance to ErrorMap (https://github.com/nipy/nipype/pull/1039)
-* ENH: Inputs with name_source can be now chained in cascade (https://github.com/nipy/nipype/pull/938)
-* ENH: Improve JSON interfaces: default settings when reading and consistent output creation
-       when writing (https://github.com/nipy/nipype/pull/1047)
-* FIX: AddCSVRow problems when using infields (https://github.com/nipy/nipype/pull/1028)
-* FIX: Removed unused ANTS registration flag (https://github.com/nipy/nipype/pull/999)
-* FIX: Amend create_tbss_non_fa() workflow to match FSL's tbss_non_fa command. (https://github.com/nipy/nipype/pull/1033)
-* FIX: remove unused mandatory flag from spm normalize (https://github.com/nipy/nipype/pull/1048)
-* ENH: Update ANTSCorticalThickness interface (https://github.com/nipy/nipype/pull/1013)
-* FIX: Edge case with sparsemodels and PEP8 cleanup (https://github.com/nipy/nipype/pull/1046)
-* ENH: New io interfaces for JSON files reading/writing (https://github.com/nipy/nipype/pull/1020)
-* ENH: Enhanced openfmri script to support freesurfer linkage (https://github.com/nipy/nipype/pull/1037)
-* BUG: matplotlib is supposed to be optional (https://github.com/nipy/nipype/pull/1003)
-* FIX: Fix split_filename behaviour when path has no file component (https://github.com/nipy/nipype/pull/1035)
-* ENH: Updated FSL dtifit to include option for grad non-linearities (https://github.com/nipy/nipype/pull/1032)
-* ENH: Updated Camino tracking interfaces, which can now use FSL bedpostx output.
-       New options also include choice of tracker, interpolator, stepsize and
-       curveinterval for angle threshold (https://github.com/nipy/nipype/pull/1029)
-* FIX: Interfaces redirecting X crashed if $DISPLAY not defined (https://github.com/nipy/nipype/pull/1027)
-* FIX: Bug crashed 'make api' (https://github.com/nipy/nipype/pull/1026)
-* ENH: Updated antsIntroduction to handle RA and RI registrations (https://github.com/nipy/nipype/pull/1009)
-* ENH: Updated N4BiasCorrection input spec to include weight image and spline order. Made
-	   argument formatting consistent. Cleaned ants.segmentation according to PEP8.
-	   (https://github.com/nipy/nipype/pull/990/files)
-* ENH: SPM12 Normalize interface (https://github.com/nipy/nipype/pull/986)
-* FIX: Utility interface test dir (https://github.com/nipy/nipype/pull/986)
-* FIX: IPython engine directory reset after crash (https://github.com/nipy/nipype/pull/987)
-* ENH: Resting state fMRI example with NiPy realignment and no SPM (https://github.com/nipy/nipype/pull/992)
-* FIX: Corrected Freesurfer SegStats _list_outputs to avoid error if summary_file is
-	   undefined (issue #994)(https://https://github.com/nipy/nipype/pull/996)
-* FIX: OpenfMRI support and FSL 5.0.7 changes (https://github.com/nipy/nipype/pull/1006)
-* FIX: Output prefix in SPM Normalize with modulation (https://github.com/nipy/nipype/pull/1023)
-* ENH: Usability improvements in cluster environments (https://github.com/nipy/nipype/pull/1025)
-* ENH: ANTs JointFusion() (https://github.com/nipy/nipype/pull/1042)
-* ENH: Added csvReader() utility (https://github.com/nipy/nipype/pull/1044)
-* FIX: typo in nipype.interfaces.freesurfer.utils.py Tkregister2 (https://github.com/nipy/nipype/pull/1083)
-* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
-* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
-* FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
-* ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)
-* FIX: Fixed AFNI Copy interface to use positional inputs as required (https://github.com/nipy/nipype/pull/1131)
-* ENH: Added a check in Dcm2nii to check if nipype created the config.ini file and remove if true (https://github.com/nipy/nipype/pull/1132)
-* ENH: Use a while loop to wait for Xvfb (up to a max wait time "xvfb_max_wait" in config file, default 10)
-       (https://github.com/nipy/nipype/pull/1142)
-
-Release 0.10.0 (October 10, 2014)
-============
-
-* ENH: New miscelaneous interfaces: SplitROIs (mapper), MergeROIs (reducer)
-       to enable parallel processing of very large images.
-* ENH: Updated FSL interfaces: BEDPOSTX and XFibres, former interfaces are still
-       available with the version suffix: BEDPOSTX4 and XFibres4. Added gpu
-       versions of BEDPOSTX: BEDPOSTXGPU, BEDPOSTX5GPU, and BEDPOSTX4GPU
-* ENH: Added experimental support for MIPAV algorithms thorugh JIST plugins
-* ENH: New dipy interfaces: Denoise, Resample
-* ENH: New Freesurfer interfaces: Tkregister2 (for conversion of fsl style matrices to freesurfer format), MRIPretess
-* ENH: New FSL interfaces: WarpPoints, WarpPointsToStd, EpiReg, ProbTrackX2, WarpUtils, ConvertWarp
-* ENH: New miscelaneous interfaces: AddCSVRow, NormalizeProbabilityMapSet, AddNoise
-* ENH: New AFNI interfaces:  Eval, Means, SVMTest, SVMTrain
-* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples
-       added to doctests, some bugs solved.
-* API: Interfaces to external packages are no longer available in the top-level
-       ``nipype`` namespace, and must be imported directly (e.g.
-       ``from nipype.interfaces import fsl``).
-* ENH: Support for elastix via a set of new interfaces: Registration, ApplyWarp,
-       AnalyzeWarp, PointsWarp, and EditTransform
-* ENH: New ANTs interface: ApplyTransformsToPoints, LaplacianThickness
-* ENH: New Diffusion Toolkit interface: TrackMerge
-* ENH: New MRtrix interface: FilterTracks
-* ENH: New metrics group in algorithms. Now Distance, Overlap, and FuzzyOverlap
-       are found in nipype.algorithms.metrics instead of misc. Overlap interface
-       extended to allow files containing multiple ROIs and volume physical units.
-* ENH: New interface in algorithms.metrics: ErrorMap (a voxel-wise diff map).
-* ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
-* ENH: Deep revision of workflows for correction of dMRI artifacts. New dmri_preprocessing
-       example.
-* ENH: New data grabbing interface that works over SSH connections, SSHDataGrabber
-* ENH: New color mode for write_graph
-* ENH: You can now force MapNodes to be run serially
-* ENH: Added ANTS based openfmri workflow
-* ENH: MapNode now supports flattening of nested lists
-* ENH: Support for headless mode using Xvfb
-* ENH: nipype_display_crash has a debugging mode
-* FIX: MRTrix tracking algorithms were ignoring mask parameters.
-* FIX: FNIRT registration pathway and associated OpenFMRI example script
-* FIX: spm12b compatibility for Model estimate
-* FIX: Batch scheduler controls the number of maximum jobs properly
-* FIX: Update for FSL 5.0.7 which deprecated Contrast Manager
-
-Release 0.9.2 (January 31, 2014)
-============
-
-* FIX: DataFinder was broken due to a typo
-* FIX: Order of DataFinder outputs was not guaranteed, it's human sorted now
-* ENH: New interfaces: Vnifti2Image, VtoMat
-
-Release 0.9.1 (December 25, 2013)
-============
-
-* FIX: installation issues
-
-Release 0.9.0 (December 20, 2013)
-============
-
-* ENH: SelectFiles: a streamlined version of DataGrabber
-* ENH: new tools for defining workflows: JoinNode, synchronize and itersource
-* ENH: W3C PROV support with optional RDF export built into Nipype
-* ENH: Added support for Simple Linux Utility Resource Management (SLURM)
-* ENH: AFNI interfaces refactor, prefix, suffix are replaced by
-       "flexible_%s_templates"
-* ENH: New SPM interfaces:
-		- spm.ResliceToReference,
-		- spm.DicomImport
-* ENH: New AFNI interfaces:
-		- afni.AFNItoNIFTI
-		- afni.TCorr1D
-* ENH: Several new interfaces related to Camino were added:
-        - camino.SFPICOCalibData
-        - camino.Conmat
-        - camino.QBallMX
-        - camino.LinRecon
-        - camino.SFPeaks
-        One outdated interface no longer part of Camino was removed:
-        - camino.Conmap
-* ENH: Three new mrtrix interfaces were added:
-        - mrtrix.GenerateDirections
-        - mrtrix.FindShPeaks
-        - mrtrix.Directions2Amplitude
-* ENH: New FSL interfaces:
-		- fsl.PrepareFieldmap
-		- fsl.TOPUP
-		- fsl.ApplyTOPUP
-		- fsl.Eddy
-* ENH: New misc interfaces:
-		- FuzzyOverlap,
-		- P2PDistance
-* ENH: New workflows: nipype.workflows.dmri.fsl.epi.[fieldmap_correction&topup_correction]
-* ENH: Added simplified outputname generation for command line interfaces.
-* ENH: Allow ants use a single mask image
-* ENH: Create configuration option for parameterizing directories with hashes
-* ENH: arrange nodes by topological sort with disconnected subgraphs
-* ENH: uses the nidm iri namespace for uuids
-* ENH: remove old reporting webpage
-* ENH: Added support for Vagrant
-
-* API: 'name' is now a positional argument for Workflow, Node, and MapNode constructors
-* API: SPM now defaults to SPM8 or SPM12b job format
-* API: DataGrabber and SelectFiles use human (or natural) sort now
-
-* FIX: Several fixes related to Camino interfaces:
-        - ProcStreamlines would ignore many arguments silently (target, waypoint, exclusion ROIS, etc.)
-        - DTLUTGen would silently round the "step", "snr" and "trace" parameters to integers
-        - PicoPDFs would not accept more than one lookup table
-        - PicoPDFs default pdf did not correspond to Camino default
-        - Track input model names were outdated (and would generate an error)
-        - Track numpds parameter could not be set for deterministic tractography
-        - FA created output files with erroneous extension
-* FIX: Deals properly with 3d files in SPM Realign
-* FIX: SPM with MCR fixed
-* FIX: Cleaned up input and output spec metadata
-* FIX: example openfmri script now makes the contrast spec a hashed input
-* FIX: FILMGLS compatibility with FSL 5.0.5
-* FIX: Freesurfer recon-all resume now avoids setting inputs
-* FIX: File removal from node respects file associations img/hdr/mat, BRIK/HEAD
-
-Release 0.8.0 (May 8, 2013)
-===========================
-
-* ENH: New interfaces: nipy.Trim, fsl.GLM, fsl.SigLoss, spm.VBMSegment, fsl.InvWarp,
-       dipy.TensorMode
-* ENH: Allow control over terminal output for commandline interfaces
-* ENH: Added preliminary support for generating Python code from Workflows.
-* ENH: New workflows for dMRI and fMRI pre-processing: added motion artifact correction
-       with rotation of the B-matrix, and susceptibility correction for EPI imaging using
-       fieldmaps. Updated eddy_correct pipeline to support both dMRI and fMRI, and new parameters.
-* ENH: Minor improvements to FSL's FUGUE and FLIRT interfaces
-* ENH: Added optional dilation of parcels in cmtk.Parcellate
-* ENH: Interpolation mode added to afni.Resample
-* ENH: Function interface can accept a list of strings containing import statements
-       that allow external functions to run without their imports defined in the
-       function body
-* ENH: Allow node configurations to override master configuration
-
-* FIX: SpecifyModel works with 3D files correctly now.
-
-Release 0.7.0 (Dec 18, 2012)
-============================
-
-* ENH: Add basic support for LSF plugin.
-* ENH: New interfaces: ICC, Meshfix, ants.Register, C3dAffineTool, ants.JacobianDeterminant,
-       afni.AutoTcorrelate, DcmStack
-* ENH: New workflows: ants template building (both using 'ANTS' and the new 'antsRegistration')
-* ENH: New examples: how to use ANTS template building workflows (smri_ants_build_tmeplate),
-	  how to set SGE specific options (smri_ants_build_template_new)
-* ENH: added no_flatten option to Merge
-* ENH: added versioning option and checking to traits
-* ENH: added deprecation metadata to traits
-* ENH: Slicer interfaces were updated to version 4.1
-
-Release 0.6.0 (Jun 30, 2012)
-============================
-
-* API: display variable no longer encoded as inputs in commandline interfaces
-
-* ENH: input hash not modified when environment DISPLAY is changed
-* ENH: support for 3d files for TSNR calculation
-* ENH: Preliminary support for graph submission with SGE, PBS and Soma Workflow
-* ENH: New interfaces: MySQLSink, nipy.Similarity, WatershedBEM, MRIsSmooth,
-       NetworkBasedStatistic, Atropos, N4BiasFieldCorrection, ApplyTransforms,
-       fs.MakeAverageSubject, epidewarp.fsl, WarpTimeSeriesImageMultiTransform,
-       AVScale, mri_ms_LDA
-* ENH: simple interfaces for spm
-
-* FIX: CompCor component calculation was erroneous
-* FIX: filename generation for AFNI and PRELUDE
-* FIX: improved slicer module autogeneration
-* FIX: added missing options for BBRegsiter
-* FIX: functionality of remove_unnecessary_ouputs cleaned up
-* FIX: local hash check works with appropriate inputs
-* FIX: Captures all stdout from commandline programs
-* FIX: Afni outputs should inherit from TraitedSpec
-
-Release 0.5.3 (Mar 23, 2012)
-============================
-
-* FIX: SPM model generation when output units is in scans
-
-Release 0.5.2 (Mar 14, 2012)
-============================
-
-* API: Node now allows specifying node level configuration for SGE/PBS clusters
-* API: Logging to file is disabled by default
-* API: New location of log file -> .nipype/nipype.cfg
-
-* ENH: Changing logging options via config works for distributed processing
-
-* FIX: Unittests on debian (logging and ipython)
-
-Release 0.5 (Mar 10, 2012)
-==========================
-
-* API: FSL defaults to Nifti when OUTPUTTYPE environment variable not found
-* API: By default inputs are removed from Node working directory
-* API: InterfaceResult class is now versioned and stores class type not instance
-* API: Added FIRST interface
-* API: Added max_jobs paramter to plugin_args. limits the number of jobs
-       executing at any given point in time
-* API: crashdump_dir is now a config execution option
-* API: new config execution options for controlling hash checking, execution and
-       logging behavior when running in distributed mode.
-* API: Node/MapNode has new attribute that allows it to run on master thread.
-* API: IPython plugin now invokes IPython 0.11 or greater
-* API: Canned workflows are now all under a different package structure
-* API: SpecifyModel event_info renamed to event_files
-* API: DataGrabber is always being rerun (unless overwrite is set to False on
-	   Node level)
-* API: "stop_on_first_rerun" does not stop for DataGrabber (unless overwrite is
-	   set to True on Node level)
-* API: Output prefix can be set for spm nodes (SliceTiming, Realign, Coregister,
-       Normalize, Smooth)
-
-* ENH: Added fsl resting state workflow based on behzadi 2007 CompCorr method.
-* ENH: TSNR node produces mean and std-dev maps; allows polynomial detrending
-* ENH: IdentityNodes are removed prior to execution
-* ENH: Added Michael Notter's beginner's guide
-* ENH: Added engine support for status callback functions
-* ENH: SPM create warped node
-* ENH: All underlying interfaces (including python ones) are now optional
-* ENH: Added imperative programming option with Nodes and caching
-* ENH: Added debug mode to configuration
-* ENH: Results can be stored and loaded without traits exceptions
-* ENH: Added concurrent log handler for distributed writing to log file
-* ENH: Reporting can be turned off using config
-* ENH: Added stats files to FreeSurferOutput
-* ENH: Support for Condor through qsub emulation
-* ENH: IdentityNode with iterable expansion takes place after remaining Identity
-       Node removal
-* ENH: Crashfile display script added
-* ENH: Added FmriRealign4d node wrapped from nipy
-* ENH: Added TBSS workflows and examples
-* ENH: Support for openfmri data processing
-* ENH: Package version check
-
-* FIX: Fixed spm preproc workflow to cater to multiple functional runs
-* FIX: Workflow outputs displays nodes with empty outputs
-* FIX: SUSAN workflow works without usans
-* FIX: SGE fixed for reading custom templates
-* FIX: warping in SPM realign, Dartel and interpolation parameters
-* FIX: Fixed voxel size parameter in freesurfer mri_convert
-* FIX: 4D images in spm coregister
-* FIX: Works around matlab tty bug
-* FIX: Overwriting connection raises exception
-* FIX: Outputs are loaded from results and not stored in memory for during
-       distributed operation
-* FIX: SPM threshold uses SPM.mat name and improved error detection
-* FIX: Removing directory contents works even when a node has no outputs
-* FIX: DARTEL workflows will run only when SPM 8 is available
-* FIX: SPM Normalize estimate field fixed
-* FIX: hashmethod argument now used for calculating hash of old file
-* FIX: Modelgen now allows FSL style event files
-
-Release 0.4.1 (Jun 16, 2011)
-============================
-
-* Minor bugfixes
-
-Release 0.4 (Jun 11, 2011)
-==========================
-
-* API: Timestamp hashing does not use ctime anymore. Please update your hashes by
-       running workflows with updatehash=True option
-       NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will
-       rerun
-* API: Workflow run function no longer supports (inseries, createdirsonly).
-       Functions used in connect string must be pickleable
-* API: SPM EstimateContrast: ignore_derivs replaced by use_derivs
-* API: All interfaces: added new config option ignore_exception
-* API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter
-       cutoff is mandatory (even if its set to np.inf). Additional interfaces
-       SpecifySPMModel and SpecifySparseModel support other types of data.
-* API: fsl.DTIFit input "save" is now called "save_tensor"
-* API: All inputs of IdentityInterfaces are mandatory by default. You can turn
-       this off by specifying mandatory_inputs=False to the constructor.
-* API: fsl FILMGLS input "autocorr_estimate" is now called "autocorr_estimate_only"
-* API: fsl ContrastMgr now requires access to specific files (no longer accepts
-       the result directory)
-* API: freesurfer.GLMFit input "surf" is now a boolean with three corresponding
-       inputs -- subject_id, hemi, and surf_geo
-
-* ENH: All commandline interfaces display stdout and stderr
-* ENH: All interfaces raise exceptions on error with an option to suppress
-* ENH: Supports a plugin interface for execution (current support for multiprocessing,
-       IPython, SGE, PBS)
-* ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS
-* ENH: Optionally allows keeping only required outputs
-* ENH: New interface: utility.Rename to change the name of files, optionally
-       using python string-formatting with inputs or regular expressions matching
-* ENH: New interface: freesurfer.ApplyMask (mri_mask)
-* ENH: New FSL interface -- SwapDimensions (fslswapdim)
-* ENH: Sparse models allow regressor scaling and temporal derivatives
-* ENH: Added support for the component parts of FSL's TBSS workflow (TBSSSkeleton
-       and DistanceMap)
-* ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images
-* ENH: Added several higher-level interfaces to the fslmaths command:
-    - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter
-      DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths
-* ENH: added support for networx 1.4 and improved iterable expansion
-* ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines
-* ENH: Ability to create a hierarchical dot file
-* ENH: Improved debugging information for rerunning nodes
-* ENH: Added 'stop_on_first_rerun' option
-* ENH: Added support for Camino
-* ENH: Added support for Camino2Trackvis
-* ENH: Added support for Connectome Viewer
-
-* BF: dcm2nii interface handles gzipped files correctly
-* BF: FNIRT generates proper outputs
-* BF: fsl.DTIFit now properly collects tensor volume
-* BF: updatehash now removes old result hash file
-
-Release 0.3.4 (Jan 12, 2011)
-============================
-
-* API: hash values for float use a string conversion up to the 10th decimal place.
-* API: Iterables in output path will always be generated as _var1_val1_var2_val2 pairs
-
-* ENH: Added support to nipy: GLM fit, contrast estimation and calculating mask from EPI
-* ENH: Added support for manipulating surface files in Freesurfer:
-    - projecting volume images onto the surface
-    - smoothing along the surface
-    - transforming a surface image from one subject to another
-    - using tksurfer to save pictures of the surface
-* ENH: Added support for flash processing using FreeSurfer
-* ENH: Added support for flirt matrix in BBRegister
-* ENH: Added support for FSL convert_xfm
-* ENH: hashes can be updated again without rerunning all nodes.
-* ENH: Added multiple regression design for FSL
-* ENH: Added SPM based Analyze to Nifti converter
-* ENH: Added increased support for PyXNAT
-* ENH: Added support for MCR-based binary version of SPM
-* ENH: Added SPM node for calculating various threshold statistics
-* ENH: Added distance and dissimilarity measurements
-
-* BF: Diffusion toolkit gets installed
-* BF: Changed FNIRT interface to accept flexible lists (rather than 4-tuples)
-      on all options specific to different subsampling levels
-
-Release 0.3.3 (Sep 16, 2010)
-============================
-
-* API: subject_id in ModelSpec is now deprecated
-* API: spm.Threshold
-  - does not need mask, beta, RPV anymore
-  - takes only one image (stat_image - mind the name change)
-  - works with SPM2 SPM.mat
-  - returns additional map - pre topological FDR
-
-* ENH: Added support for Diffusion toolkit
-* ENH: Added support for FSL slicer and overlay
-* ENH: Added support for dcm2nii
-
-* BF: DataSink properly handles lists of lists now
-* BF: DataGrabber has option for raising Exception on getting empty lists
-* BF: Traits logic for 'requires' metadata
-* BF: allows workflows to be relocatable
-* BF: nested workflows with connections don't raise connection not found error
-* BF: multiple workflows with identical nodenames and iterables do not create nestsed workflows
-
-Release 0.3.2 (Aug 03, 2010)
-============================
-
-Enhancements
-------------
-
-  - all outputs from nodes are now pickled as part of workflow processing
-  - added git developer docs
-
-Bugs fixed
-----------
-
-* FreeSurfer
-
-  - Fixed bugs in SegStats doctest
-
-Release 0.3.1 (Jul 29, 2010)
-============================
-
-Bugs fixed
-----------
-
-* FreeSurfer
-
-  - Fixed bugs in glmfit and concatenate
-  - Added group t-test to freesurfer tutorial
-
-Release 0.3 (Jul 27, 2010)
-==========================
-
-Incompatible changes
---------------------
-
-* Complete redesign of the Interface class - heavy use of Traits.
-
-* Changes in the engine API - added Workflow and MapNode. Compulsory name argument.
-
-Features added
---------------
-
-* General:
-
-  - Type checking of inputs and outputs using Traits from ETS_.
-  - Support for nested workflows.
-  - Preliminary Slicer and AFNI support.
-  - New flexible DataGrabber node.
-  - AtlasPick and Threshold nodes.
-  - Preliminary support for XNAT.
-  - Doubled number of the tutorials.
-
-* FSL:
-
-  - Added DTI processing nodes (note that TBSS nodes are still experimental).
-  - Recreated FEAT workflow.
-
-* SPM:
-
-  - Added New Segment and many other nodes.
-  - Redesigned second level analysis.
diff --git a/doc/users/debug.rst b/doc/users/debug.rst
index 91aa3b6f2f..303df9f82a 100644
--- a/doc/users/debug.rst
+++ b/doc/users/debug.rst
@@ -42,6 +42,9 @@ performance issues.
 #. All Nipype crashfiles can be inspected with the `nipype_display_crash`
    utility.
 
+#. The `nipype_crash_search` command allows you to search for regular expressions
+in the tracebacks of the Nipype crashfiles within a log folder.
+
 #. Nipype determines the hash of the input state of a node. If any input
    contains strings that represent files on the system path, the hash evaluation
    mechanism will determine the timestamp or content hash of each of those