update variable names

Author: josephmje

nipype/interfaces/fsl/epi.py

@@ -675,8 +675,6 @@ class EddyInputSpec(FSLCommandInputSpec):
         desc="Do NOT perform a post-eddy alignment of " "shells",
     )
     fwhm = traits.Float(
-        default_value=0.0,
-        usedefault=True,
         desc=("FWHM for conditioning filter when estimating " "the parameters"),
         argstr="--fwhm=%s",
     )
@@ -740,7 +738,7 @@ class EddyInputSpec(FSLCommandInputSpec):
         desc=(
             "Multi-band offset (-1 if bottom slice removed, 1 if " "top slice removed"
         ),
-        requires=["mb"],
+        requires=["multiband_factor"],
         min_ver="5.0.10",
     )
 
@@ -750,27 +748,27 @@ class EddyInputSpec(FSLCommandInputSpec):
         requires=["use_cuda"],
         min_ver="5.0.11",
     )
-    slice2vol_iterations = traits.Int(
-        argstr="--s2v_niter=%s",
+    slice2vol_niter = traits.Int(
+        argstr="--s2v_niter=%d",
         desc="Number of iterations for slice-to-vol",
         requires=["mporder"],
         min_ver="5.0.11",
     )
-    s2v_lambda = traits.Int(
-        agstr="--s2v_lambda",
+    slice2vol_lambda = traits.Int(
+        argstr="--s2v_lambda=%d",
         desc="Regularisation weight for slice-to-vol movement (reasonable range 1-10)",
         requires=["mporder"],
         min_ver="5.0.11",
     )
-    s2v_interp = traits.Enum(
+    slice2vol_interp = traits.Enum(
         "trilinear",
         "spline",
         argstr="--s2v_interp=%s",
         desc="Slice-to-vol interpolation model for estimation step",
         requires=["mporder"],
         min_ver="5.0.11",
     )
-    slspec = traits.File(
+    slice_order = traits.File(
         exists=True,
         argstr="--slspec=%s",
         desc="Name of text file completely specifying slice/group acquisition",
@@ -783,7 +781,7 @@ class EddyInputSpec(FSLCommandInputSpec):
         argstr="--json=%s",
         desc="Name of .json text file with information about slice timing",
         requires=["mporder"],
-        xor=["slspec"],
+        xor=["slice_order"],
         min_ver="6.0.1",
     )
 
@@ -961,7 +959,7 @@ class Eddy(FSLCommand):
     Running eddy on an Nvidia GPU using cuda:
     >>> eddy.inputs.use_cuda = True
     >>> eddy.cmdline # doctest: +ELLIPSIS
-    'eddy_cuda --flm=quadratic --ff=10.0 --fwhm=0.0 \
+    'eddy_cuda --flm=quadratic --ff=10.0 \
 --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 \
@@ -970,7 +968,7 @@ class Eddy(FSLCommand):
     Running eddy on a CPU using OpenMP:
     >>> eddy.inputs.use_cuda = False
     >>> eddy.cmdline          # doctest: +ELLIPSIS
-    'eddy_openmp --flm=quadratic --ff=10.0 --fwhm=0.0 \
+    'eddy_openmp --flm=quadratic --ff=10.0 \
 --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 \
@@ -979,17 +977,17 @@ class Eddy(FSLCommand):
     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.inputs.slice2vol_niter = 5
+    >>> eddy.inputs.slice2vol_lambda = 1
+    >>> eddy.inputs.slice2vol_interp = 'trilinear'
+    >>> eddy.inputs.slice_order = 'epi_slspec.txt'
     >>> eddy.cmdline          # doctest: +ELLIPSIS
-    'eddy_cuda --flm=quadratic --ff=10.0 --fwhm=0.0 \
+    'eddy_cuda --flm=quadratic --ff=10.0 \
 --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'
+--out=.../eddy_corrected --s2v_interp=trilinear --s2v_lambda=1 \
+--s2v_niter=5 --slspec=epi_slspec.txt --slm=none'
     >>> res = eddy.run()     # doctest: +SKIP
 
     """

nipype/interfaces/fsl/tests/test_auto_Eddy.py

@@ -17,7 +17,7 @@ def test_Eddy_inputs():
         field_mat=dict(argstr="--field_mat=%s", extensions=None,),
         flm=dict(argstr="--flm=%s", usedefault=True,),
         fudge_factor=dict(argstr="--ff=%s", usedefault=True,),
-        fwhm=dict(argstr="--fwhm=%s", usedefault=True,),
+        fwhm=dict(argstr="--fwhm=%s",),
         in_acqp=dict(argstr="--acqp=%s", extensions=None, mandatory=True,),
         in_bval=dict(argstr="--bvals=%s", extensions=None, mandatory=True,),
         in_bvec=dict(argstr="--bvecs=%s", extensions=None, mandatory=True,),
@@ -32,10 +32,11 @@ def test_Eddy_inputs():
         interp=dict(argstr="--interp=%s", usedefault=True,),
         is_shelled=dict(argstr="--data_is_shelled",),
         json=dict(
-            argstr="--json=%s", min_ver="6.0.1", requires=["mporder"], xor=["slspec"],
+            argstr="--json=%s",
+            min_ver="6.0.1",
+            requires=["mporder"],
+            xor=["slice_order"],
         ),
-        mb=dict(argstr="--mb=%s", min_ver="5.0.10",),
-        mb_offs=dict(argstr="--mb_offs=%s", min_ver="5.0.10", requires=["mb"],),
         mbs_ksp=dict(
             argstr="--mbs_ksp=%smm",
             min_ver="6.0.1",
@@ -53,6 +54,10 @@ def test_Eddy_inputs():
         ),
         method=dict(argstr="--resamp=%s", usedefault=True,),
         mporder=dict(argstr="--mporder=%s", min_ver="5.0.11", requires=["use_cuda"],),
+        multiband_factor=dict(argstr="--mb=%s", min_ver="5.0.10",),
+        multiband_offset=dict(
+            argstr="--mb_offs=%d", min_ver="5.0.10", requires=["multiband_factor"],
+        ),
         niter=dict(argstr="--niter=%s", usedefault=True,),
         num_threads=dict(nohash=True, usedefault=True,),
         nvoxhp=dict(argstr="--nvoxhp=%s", usedefault=True,),
@@ -65,18 +70,20 @@ def test_Eddy_inputs():
         output_type=dict(),
         repol=dict(argstr="--repol",),
         residuals=dict(argstr="--residuals", min_ver="5.0.10",),
-        s2v_interp=dict(
+        session=dict(argstr="--session=%s", extensions=None,),
+        slice2vol_interp=dict(
             argstr="--s2v_interp=%s", min_ver="5.0.11", requires=["mporder"],
         ),
-        s2v_lambda=dict(agstr="--s2v_lambda", min_ver="5.0.11", requires=["mporder"],),
-        s2v_niter=dict(
-            argstr="--s2v_niter=%s", min_ver="5.0.11", requires=["mporder"],
+        slice2vol_lambda=dict(
+            argstr="--s2v_lambda=%d", min_ver="5.0.11", requires=["mporder"],
         ),
-        session=dict(argstr="--session=%s", extensions=None,),
-        slm=dict(argstr="--slm=%s", usedefault=True,),
-        slspec=dict(
+        slice2vol_niter=dict(
+            argstr="--s2v_niter=%d", min_ver="5.0.11", requires=["mporder"],
+        ),
+        slice_order=dict(
             argstr="--slspec=%s", min_ver="5.0.11", requires=["mporder"], xor=["json"],
         ),
+        slm=dict(argstr="--slm=%s", usedefault=True,),
         use_cuda=dict(),
     )
     inputs = Eddy.input_spec()