fixing paths for fmri_spm_dartel and fmri_spm_nested

Author: oesteban

circle.yml

@@ -7,8 +7,8 @@ dependencies:
     - "~/docker"
 
   pre:
-    - pip install coverage
     - mkdir -p "~/scratch/nose"
+
   override:
     - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
     - docker build -t nipype/testbench:latest . :

examples/fmri_spm_dartel.py

@@ -264,7 +264,7 @@
 datasource = pe.Node(nio.DataGrabber(infields=['subject_id'],
                                                outfields=['func', 'struct']),
                      name='datasource')
-datasource.inputs.template = '%s/%s.nii'
+datasource.inputs.template = 'nipype-tutorial/data/%s/%s.nii'
 datasource.inputs.template_args = info
 datasource.inputs.sort_filelist = True
 
@@ -275,7 +275,7 @@
                                                          outfields=['struct']),
                                name='datasource_dartel',
                                iterfield=['subject_id'])
-datasource_dartel.inputs.template = '%s/%s.nii'
+datasource_dartel.inputs.template = 'nipype-tutorial/data/%s/%s.nii'
 datasource_dartel.inputs.template_args = dict(struct=[['subject_id', 'struct']])
 datasource_dartel.inputs.sort_filelist = True
 datasource_dartel.inputs.subject_id = subject_list

examples/fmri_spm_nested.py

@@ -56,8 +56,18 @@
 and shared across users, projects and labs.
 
 
-Setup preprocessing workflow
-----------------------------
+Example of how to inline functions in connect()
+-----------------------------------------------
+
+"""
+def _template_path(in_data):
+    return op.abspath(op.join(in_data, 'nipype-tutorial/data/T1.nii'))
+
+
+"""
+
+Set-up preprocessing workflow
+-----------------------------
 
 This is a generic preprocessing workflow that can be used by different analyses
 
@@ -482,13 +492,6 @@ def getstripdir(subject_id):
                                                  ('residual_image', 'residual_image')]),
                     ])
 
-"""
-Inlining functions in connect()
--------------------------------
-"""
-def _template_path(in_data):
-    return op.abspath(op.join(in_data, 'nipype-tutorial/data/T1.nii'))
-
 
 """
 Execute the second level pipeline