From 2951749f54d357a7a0b36f1c23f65d51b68172b7 Mon Sep 17 00:00:00 2001
From: Ian Malone <i.malone@ucl.ac.uk>
Date: Mon, 24 Apr 2017 15:33:57 +0100
Subject: [PATCH] [ENH] FSL epi interface, add missing Eddy options.

---
 nipype/interfaces/fsl/epi.py                  | 26 +++++++++++++++++++
 nipype/interfaces/fsl/tests/test_auto_Eddy.py | 17 ++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py
index 2b45d62c2d..23aa1ed974 100644
--- a/nipype/interfaces/fsl/epi.py
+++ b/nipype/interfaces/fsl/epi.py
@@ -423,6 +423,32 @@ class EddyInputSpec(FSLCommandInputSpec):
     flm = traits.Enum('linear', 'quadratic', 'cubic', argstr='--flm=%s',
                       desc='First level EC model')
 
+    slm = traits.Enum('none', 'linear', 'quadratic', argstr='--slm=%s',
+                      desc='Second level EC model')
+
+    fep = traits.Bool(False, argstr='--fep',
+                      desc='Fill empty planes in x- or y-directions')
+
+    interp = traits.Enum('spline', 'trilinear', argstr='--interp=%s',
+                         desc='Interpolation model for estimation step')
+
+    nvoxhp = traits.Int(1000, argstr='--nvoxhp=%s',
+                        desc=('# of voxels used to estimate the '
+                              'hyperparameters'))
+
+    fudge_factor = traits.Float(10.0, argstr='--ff=%s',
+                                desc=('Fudge factor for hyperparameter '
+                                      'error variance'))
+
+    dont_sep_offs_move = traits.Bool(False, argstr='--dont_sep_offs_move',
+                                     desc=('Do NOT attempt to separate '
+                                           'field offset from subject '
+                                           'movement'))
+
+    dont_peas = traits.Bool(False, argstr='--dont_peas',
+                           desc="Do NOT perform a post-eddy alignment of "
+                                "shells")
+
     fwhm = traits.Float(desc=('FWHM for conditioning filter when estimating '
                               'the parameters'), argstr='--fwhm=%s')
 
diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py
index 08e0135d00..e47633fb07 100644
--- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py
+++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py
@@ -6,15 +6,23 @@
 def test_Eddy_inputs():
     input_map = dict(args=dict(argstr='%s',
     ),
+    dont_peas=dict(argstr='--dont_peas',
+    ),
+    dont_sep_offs_move=dict(argstr='--dont_sep_offs_move',
+    ),
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    fep=dict(argstr='--fep',
+    ),
     field=dict(argstr='--field=%s',
     ),
     field_mat=dict(argstr='--field_mat=%s',
     ),
     flm=dict(argstr='--flm=%s',
     ),
+    fudge_factor=dict(argstr='--ff=%s',
+    ),
     fwhm=dict(argstr='--fwhm=%s',
     ),
     ignore_exception=dict(nohash=True,
@@ -43,6 +51,8 @@ def test_Eddy_inputs():
     ),
     in_topup_movpar=dict(requires=['in_topup_fieldcoef'],
     ),
+    interp=dict(argstr='--interp=%s',
+    ),
     is_shelled=dict(argstr='--data_is_shelled',
     ),
     method=dict(argstr='--resamp=%s',
@@ -52,6 +62,8 @@ def test_Eddy_inputs():
     num_threads=dict(nohash=True,
     usedefault=True,
     ),
+    nvoxhp=dict(argstr='--nvoxhp=%s',
+    ),
     out_base=dict(argstr='--out=%s',
     usedefault=True,
     ),
@@ -60,6 +72,8 @@ def test_Eddy_inputs():
     ),
     session=dict(argstr='--session=%s',
     ),
+    slm=dict(argstr='--slm=%s',
+    ),
     terminal_output=dict(nohash=True,
     ),
     use_cuda=dict(),
@@ -74,6 +88,9 @@ def test_Eddy_inputs():
 def test_Eddy_outputs():
     output_map = dict(out_corrected=dict(),
     out_movement_rms=dict(),
+    out_outlier_map=dict(),
+    out_outlier_n_sd_map=dict(),
+    out_outlier_n_sqr_sd_map=dict(),
     out_outlier_report=dict(),
     out_parameter=dict(),
     out_restricted_movement_rms=dict(),