Merge pull request #403 from satra/fix/test

fix: examples

Author: satra

examples/fmri_fsl_reuse.py

@@ -17,15 +17,6 @@
 
 import os                                    # system functions
 
-"""
-.. note::
-    config for logging should be set before anything else
-"""
-
-from nipype.utils.config import config
-config.set('logging', 'log_to_file', 'false')
-config.set_log_dir(os.getcwd())
-
 import nipype.interfaces.io as nio           # Data i/o
 import nipype.interfaces.fsl as fsl          # fsl
 import nipype.interfaces.utility as util     # utility

examples/amri_freesurfer.py renamed to examples/smri_freesurfer.py

@@ -1,16 +1,36 @@
+#!/usr/bin/env python
+"""
+================
+sMRI: FreeSurfer
+================
+
+This script, smri_freesurfer.py, demonstrates the ability to call reconall on
+a set of subjects and then make an average subject.
+
+    python smri_freesurfer.py
+
+Import necessary modules from nipype.
+"""
+
+import os
+
 import nipype.pipeline.engine as pe
 import nipype.interfaces.io as nio
-import os
 from nipype.interfaces.freesurfer.preprocess import ReconAll
 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',
@@ -20,6 +40,10 @@
 datasource.inputs.template_args = dict(struct=[['subject_id', 'struct']])
 datasource.inputs.subject_id = subject_list
 
+"""
+Run recon-all
+"""
+
 recon_all = pe.MapNode(interface=ReconAll(), name='recon_all',
                        iterfield=['subject_id', 'T1_files'])
 recon_all.inputs.subject_id = subject_list
@@ -29,6 +53,10 @@
 
 wf.connect(datasource, 'struct', recon_all, 'T1_files')
 
+"""
+Make average subject
+"""
+
 average = pe.Node(interface=MakeAverageSubject(), name="average")
 average.inputs.subjects_dir = subjects_dir