Python version of changes

170327-nipype/notebooks/rfmri_group_1/PreprocessingWorkflow.py

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+
+# coding: utf-8
+
+# In[1]:
+
+# Import workflow elements
+from nipype import Node, Workflow
+
+
+# In[2]:
+
+# Import necessary interfaces
+from nipype.interfaces import fsl, afni
+
+
+# In[19]:
+
+#Define workflow and create nodes
+wf = Workflow(name="group1_pre_process")
+wf.base_dir = 'group1_results'
+
+#Skullstrip
+node_skull_strip = Node(fsl.BET(functional=True), name='bet')
+
+#FLIRT
+node_volreg = Node(fsl.MCFLIRT(), name='volreg')
+
+#Volreg AFNI
+node_afni_volreg = Node(afni.Volreg(), name='volreg_afni')
+
+
+
+# In[20]:
+
+#Connet nodes
+wf.connect(node_skull_strip, 'out_file', node_volreg,'in_file')
+wf.connect(node_skull_strip, 'out_file', node_afni_volreg,'in_file')
+
+
+# In[21]:
+
+node_afni_volreg.help()
+
+
+# In[22]:
+
+wf.inputs.bet.in_file = "/home/jovyan/work/data/ds000114/sub-01/func/sub-01_task-linebisection_bold.nii.gz"
+wf.run()
+
+
+# In[23]:
+
+from IPython.display import Image
+Image(wf.write_graph())
+
+
+# In[ ]:
+
+
+
+
+# In[ ]:
+
+
+