Merge pull request #24 from nipy/master

Re-base with nipy master

Author: pintohutch

LICENSE

@@ -1,30 +1,15 @@
-Copyright (c) 2009-2014, NIPY Developers
-All rights reserved.
+Copyright (c) 2009-2016, Nipype developers
 
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
 
-    * Redistributions of source code must retain the above copyright
-       notice, this list of conditions and the following disclaimer.
+    http://www.apache.org/licenses/LICENSE-2.0
 
-    * Redistributions in binary form must reproduce the above
-       copyright notice, this list of conditions and the following
-       disclaimer in the documentation and/or other materials provided
-       with the distribution.
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
-    * Neither the name of the NIPY Developers nor the names of any
-       contributors may be used to endorse or promote products derived
-       from this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+Prior to release 0.12, Nipype was licensed under a BSD license.

doc/users/debug.rst

@@ -43,7 +43,7 @@ performance issues.
    utility.
 
 #. The `nipype_crash_search` command allows you to search for regular expressions
-in the tracebacks of the Nipype crashfiles within a log folder.
+   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

examples/smri_fsreconall.py

@@ -5,11 +5,14 @@
 ================
 
 This script, smri_fsreconall.py, demonstrates the ability to use the
-reconall nipype workflow with a set of subjects and then make an average
-subject::
+create_reconall_workflow function to create a workflow and then run it on a
+set of subjects and then make an average subject::
 
     python smri_fsreconall.py
 
+For an example on how to call FreeSurfer's reconall script in Nipype
+see smri_freesurfer.py.
+
 Import necessary modules from nipype.
 """
 

nipype/info.py

@@ -56,7 +56,7 @@ def get_nipype_gitversion():
 CLASSIFIERS = ["Development Status :: 5 - Production/Stable",
                "Environment :: Console",
                "Intended Audience :: Science/Research",
-               "License :: OSI Approved :: BSD License",
+               "License :: OSI Approved :: Apache Software License",
                "Operating System :: MacOS :: MacOS X",
                "Operating System :: POSIX :: Linux",
                "Programming Language :: Python :: 2.7",
@@ -85,12 +85,12 @@ def get_nipype_gitversion():
 to existing neuroimaging software and facilitates interaction between
 these packages within a single workflow. Nipype provides an environment
 that encourages interactive exploration of algorithms from different
-packages (e.g., ANTS, SPM, FSL, FreeSurfer, Camino, MRtrix, MNE, AFNI, BRAINS,
-Slicer), eases the design of workflows within and between packages, and
-reduces the learning curve necessary to use different packages. Nipype is
-creating a collaborative platform for neuroimaging software development
-in a high-level language and addressing limitations of existing pipeline
-systems.
+packages (e.g., AFNI, ANTS, BRAINS, BrainSuite, Camino, FreeSurfer, FSL, MNE,
+MRtrix, MNE, Nipy, Slicer, SPM), eases the design of workflows within and
+between packages, and reduces the learning curve necessary to use different
+packages. Nipype is creating a collaborative platform for neuroimaging software
+development in a high-level language and addressing limitations of existing
+pipeline systems.
 
 *Nipype* allows you to:
 
@@ -121,7 +121,7 @@ def get_nipype_gitversion():
 LONG_DESCRIPTION = long_description
 URL = "http://nipy.org/nipype"
 DOWNLOAD_URL = "http://github.com/nipy/nipype/archives/master"
-LICENSE = "BSD license"
+LICENSE = "Apache License, 2.0"
 CLASSIFIERS = CLASSIFIERS
 AUTHOR = "nipype developers"
 AUTHOR_EMAIL = "neuroimaging@python.org"

nipype/interfaces/dcm2nii.py

@@ -292,7 +292,7 @@ def _parse_stdout(self, stdout):
                         bvals.append(out_file + ".bval")
                         find_b = False
                 # next scan will have bvals/bvecs
-                elif 'DTI gradient directions' in line:
+                elif 'DTI gradients' in line or 'DTI gradient directions' in line:
                     find_b = True
                 else:
                     pass

nipype/workflows/smri/freesurfer/recon.py

@@ -81,7 +81,11 @@ def link_masks(subjects_dir, subject_id):
     return wf
 
 def create_reconall_workflow(name="ReconAll", plugin_args=None):
-    """Creates the ReconAll workflow in nipype.
+    """Creates the ReconAll workflow in Nipype. This workflow is designed to
+    run the same commands as FreeSurfer's reconall script but with the added
+    features that a Nipype workflow provides. Before running this workflow, it
+    is necessary to have the FREESURFER_HOME environmental variable set to the
+    directory containing the version of FreeSurfer to be used in this workflow.
 
     Example
     -------