ENH: Starting to add workflows to nipype.

Author: David Ellis

examples/smri_fsreconall.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+"""
+================
+sMRI: FreeSurfer
+================
+
+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
+
+
+subject_list = ['s1', 's3']
+data_dir = os.path.abspath('data')
+subjects_dir = os.path.abspath('amri_freesurfer_tutorial/subjects_dir')
+
+wf = pe.Workflow(name="l1workflow")
+wf.base_dir = os.path.abspath('amri_freesurfer_tutorial/workdir')
+
+"""
+Grab data
+"""
+
+datasource = pe.MapNode(interface=nio.DataGrabber(infields=['subject_id'],
+                                                  outfields=['struct']),
+                        name='datasource',
+                        iterfield=['subject_id'])
+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
+
+"""
+Run recon-all
+"""
+
+recon_all = create_reconall_workflow(subjects_dir=subjects_dir)
+pe.MapNode(interface=ReconAllWF(), name='recon_all',
+                       iterfield=['subject_id', 'T1_files'])
+recon_all.inputs.subject_id = subject_list
+if not os.path.exists(subjects_dir):
+    os.mkdir(subjects_dir)
+recon_all.inputs.subjects_dir = subjects_dir
+
+wf.connect(datasource, 'struct', recon_all, 'T1_files')
+
+"""
+Make average subject
+"""
+
+average = pe.Node(interface=MakeAverageSubject(), name="average")
+average.inputs.subjects_dir = subjects_dir
+
+wf.connect(recon_all, 'subject_id', average, 'subjects_ids')
+
+wf.run("MultiProc", plugin_args={'n_procs': 4})