testspmpreproc.py

import os

import numpy as np

from nipype.interfaces.spm import *
import nipype.interfaces.matlab as mlab      # how to run matlab

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

func = os.path.abspath('../testdata/testfunc.nii')
meanfunc = os.path.abspath('../testdata/meantestfunc.nii')
struct = os.path.abspath('../testdata/struct.nii')

print 'testing slicetiming'
res1 = SliceTiming(in_files=func,
                   num_slices=35,
                   slice_order = range(1,36),
                   ref_slice=1,
                   time_repetition=3.,
                   time_acquisition=3.-3./35.).run()
assert(res1.runtime.returncode == 0)
print 'testing realign'
res2 = Realign(in_files=func).run()
assert(res2.runtime.returncode == 0)
print 'testing smooth'
res3 = Smooth(in_files=func).run()
assert(res3.runtime.returncode == 0)
print 'testing coregister'
res4 = Coregister(target=struct,source=meanfunc,apply_to_files=func).run()
assert(res4.runtime.returncode == 0)
print 'testing normalize'
res5 = Normalize(template='/software/spm8/templates/T1.nii',
                 source=struct).run()
assert(res5.runtime.returncode == 0)
print 'testing segment'
res6 = Segment(data=struct).run()
assert(res6.runtime.returncode == 0)
print 'testing new segment'
res7 = NewSegment(channel_files=struct).run()
assert(res7.runtime.returncode == 0)