runs a simple spm job on the sge cluster

sge_example.py

"""Example script that executes via SGE qsub
"""
import nipype.pipeline.engine as pe
import nipype.interfaces.matlab as mlab
import nipype.interfaces.spm as spm
import os

mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodesktop -nosplash")
mlab.MatlabCommand.set_default_paths('/software/spm8')

segment = pe.Node(interface=spm.Segment(), name="segment")

# ensure that the folder data exists and there is a T1.nii file there
segment.inputs.data = os.path.abspath("data/T1.nii")
segment.inputs.gm_output_type = [True, True, True]
segment.inputs.wm_output_type = [True, True, True]

smooth_gm = pe.Node(interface=spm.Smooth(), name="smooth_gm")

workflow = pe.Workflow(name="workflow_cleanup_test")
workflow.base_dir = os.getcwd()
workflow.connect(segment, 'native_gm_image', smooth_gm, 'in_files')

# -V ensures environment variables are sent over and -q chooses the queue
workflow.config.update(sgeargs='-V -q testqueue')

# run the workflow - assumes you can execute qsub from the 
# current machine and that the filesystem is shared between 
# the current machine and the SGE cluster.
workflow.run(plugin='SGE')