add doctest for running eddy with s2v motion correction

Author: josephmje

nipype/interfaces/fsl/epi.py

@@ -727,6 +727,7 @@ class EddyInputSpec(FSLCommandInputSpec):
     mporder = traits.Int(
         argstr='--mporder=%s',
         desc='Order of slice-to-vol movement model',
+        requires=['use_cuda'],
         min_ver='5.0.11')
     s2v_niter = traits.Int(
         argstr='--s2v_niter=%s',
@@ -885,6 +886,8 @@ class Eddy(FSLCommand):
     --------
 
     >>> from nipype.interfaces.fsl import Eddy
+
+    Running eddy on an Nvidia GPU using cuda:
     >>> eddy = Eddy()
     >>> eddy.inputs.in_file = 'epi.nii'
     >>> eddy.inputs.in_mask  = 'epi_mask.nii'
@@ -899,14 +902,31 @@ class Eddy(FSLCommand):
 --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
 --interp=spline --resamp=jac --niter=5 --nvoxhp=1000 \
 --out=.../eddy_corrected --slm=none'
+
+    Running eddy on a CPU using OpenMP:
     >>> eddy.inputs.use_cuda = False
-    >>> eddy.cmdline # doctest: +ELLIPSIS
+    >>> eddy.cmdline          # doctest: +ELLIPSIS
     'eddy_openmp --flm=quadratic --ff=10.0 --fwhm=0.0 \
 --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
 --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
 --interp=spline --resamp=jac --niter=5 --nvoxhp=1000 \
 --out=.../eddy_corrected --slm=none'
-    >>> res = eddy.run() # doctest: +SKIP
+
+    Running eddy with slice-to-volume motion correction:
+    >>> eddy.inputs.use_cuda = True
+    >>> eddy.inputs.mporder = 6
+    >>> eddy.inputs.s2v_niter = 5
+    >>> eddy.inputs.s2v_lambda = 1
+    >>> eddy.inputs.s2v_interp = 'trilinear'
+    >>> eddy.inputs.slspec = 'epi_slspec.txt'
+    >>> eddy.cmdline          # doctest: +ELLIPSIS
+    'eddy_cuda --flm=quadratic --ff=10.0 --fwhm=0.0 \
+--acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \
+--imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \
+--interp=spline --resamp=jac --mporder=6 --niter=5 --nvoxhp=1000 \
+--out=.../eddy_corrected --s2v_interp=trilinear --s2v_niter=5 \
+--slm=none --slspec=epi_slspec.txt'
+    >>> res = eddy.run()     # doctest: +SKIP
 
     """
 

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -125,6 +125,7 @@ def test_Eddy_inputs():
         mporder=dict(
             argstr='--mporder=%s',
             min_ver='5.0.11',
+            requires=['use_cuda'],
         ),
         niter=dict(
             argstr='--niter=%s',