Merge remote-tracking branch 'upstream/master' into ucsf_sge

Author: akeshavan

CHANGES

@@ -1,6 +1,7 @@
 Next release
 ============
 
+* 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)
 * FIX: Prevent crash when tvtk is loaded - ETS_TOOLKIT=null (https://github.com/nipy/nipype/pull/973)
@@ -25,6 +26,8 @@ Next release
 * 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)
+* FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
 
 Release 0.11.0 (September 15, 2015)
 ============

CHANGES.orig

@@ -20,19 +20,20 @@ $script = <<SCRIPT
 # qconf -aattr queue slots "2, [neuro=3]" main.q
 
 # install anaconda
-wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
 chmod +x miniconda.sh
 ./miniconda.sh -b
-echo "export PATH=$HOME/miniconda/bin:\\$PATH" >> .bashrc
+echo "export PATH=$HOME/miniconda3/bin:\\$PATH" >> .bashrc
 
 # install nipype dependencies
-$HOME/miniconda/bin/conda update --yes conda
-$HOME/miniconda/bin/conda install --yes pip numpy scipy nose traits networkx
-$HOME/miniconda/bin/conda install --yes dateutil ipython-notebook matplotlib
-$HOME/miniconda/bin/pip install nibabel --use-mirrors
-$HOME/miniconda/bin/pip install https://github.com/RDFLib/rdflib/archive/master.zip
-$HOME/miniconda/bin/pip install https://github.com/trungdong/prov/archive/rdf.zip
-$HOME/miniconda/bin/pip install https://github.com/nipy/nipype/archive/master.zip
+$HOME/miniconda3/bin/conda update --yes conda
+$HOME/miniconda3/bin/conda install --yes pip scipy nose networkx lxml future simplejson
+$HOME/miniconda3/bin/conda install --yes python-dateutil jupyter matplotlib
+$HOME/miniconda3/bin/pip install nibabel
+$HOME/miniconda3/bin/pip install prov
+$HOME/miniconda3/bin/pip install xvfbwrapper
+$HOME/miniconda3/bin/pip install traits
+$HOME/miniconda3/bin/pip install https://github.com/nipy/nipype/archive/master.zip
 SCRIPT
 
 Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|

Vagrantfile

@@ -0,0 +1,90 @@
+#!/usr/bin/env python
+"""
+================
+sMRI: FSReconAll
+================
+
+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::
+
+    python smri_fsreconall.py
+
+Import necessary modules from nipype.
+"""
+
+import os
+
+import nipype.pipeline.engine as pe
+import nipype.interfaces.io as nio
+from nipype.workflows.smri.freesurfer import create_reconall_workflow
+from nipype.interfaces.freesurfer.utils import MakeAverageSubject
+from nipype.interfaces.utility import IdentityInterface
+
+"""
+Assign the tutorial directory
+"""
+
+tutorial_dir = os.path.abspath('smri_fsreconall_tutorial')
+if not os.path.isdir(tutorial_dir):
+    os.mkdir(tutorial_dir)
+
+"""
+Define the workflow directories
+"""
+
+subject_list = ['s1', 's3']
+data_dir = os.path.abspath('data')
+subjects_dir = os.path.join(tutorial_dir, 'subjects_dir')
+if not os.path.exists(subjects_dir):
+    os.mkdir(subjects_dir)
+
+wf = pe.Workflow(name="l1workflow")
+wf.base_dir = os.path.join(tutorial_dir, 'workdir')
+
+"""
+Create inputspec
+"""
+
+inputspec = pe.Node(interface=IdentityInterface(['subject_id']),
+                    name="inputspec")
+inputspec.iterables = ("subject_id", subject_list)
+
+"""
+Grab data
+"""
+
+datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],
+                                               outfields=['struct']),
+                        name='datasource')
+datasource.inputs.base_directory = data_dir
+datasource.inputs.template = '%s/%s.nii'
+datasource.inputs.template_args = dict(struct=[['subject_id', 'struct']])
+datasource.inputs.subject_id = subject_list
+datasource.inputs.sort_filelist = True
+
+wf.connect(inputspec, 'subject_id', datasource, 'subject_id')
+
+"""
+Run recon-all
+"""
+
+recon_all = create_reconall_workflow()
+recon_all.inputs.inputspec.subjects_dir = subjects_dir
+
+wf.connect(datasource, 'struct', recon_all, 'inputspec.T1_files')
+wf.connect(inputspec, 'subject_id', recon_all, 'inputspec.subject_id')
+
+"""
+Make average subject
+"""
+
+average = pe.JoinNode(interface=MakeAverageSubject(),
+                      joinsource="inputspec",
+                      joinfield="subjects_ids",
+                      name="average")
+average.inputs.subjects_dir = subjects_dir
+
+wf.connect(recon_all, 'postdatasink_outputspec.subject_id', average, 'subjects_ids')
+
+wf.run("MultiProc", plugin_args={'n_procs': 4})

examples/smri_fsreconall.py

@@ -828,7 +828,7 @@ class DenoiseImageInputSpec(ANTSCommandInputSpec):
 
 class DenoiseImageOutputSpec(TraitedSpec):
     output_image = File(exists=True)
-    noise_image = File(exists=True)
+    noise_image = File()
 
 
 class DenoiseImage(ANTSCommand):

nipype/algorithms/tests/test_auto_Overlap.py

@@ -0,0 +1,2 @@
+from .brainsuite import (Bse, Bfc, Pvc, Cerebro, Cortex, Scrubmask, Tca,
+                         Dewisp, Dfs, Pialmesh, Skullfinder, Hemisplit)