From f46fb75574d9102b72c4b7067302155d0306035b Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 11 Jun 2014 12:32:41 +0200
Subject: [PATCH 01/11] Bugfix in FUGUE and doctest added

FUGUE interface was adding wrong parameter in forward warping mode.
Added the missing doctest of the interface.
---
 CHANGES                                       |  1 +
 nipype/interfaces/fsl/preprocess.py           | 41 ++++++++++++-------
 .../interfaces/fsl/tests/test_auto_FUGUE.py   |  1 -
 3 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/CHANGES b/CHANGES
index f4ebb73be0..4fb242cb24 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,6 +1,7 @@
 Next Release
 ============
 
+* FIX: FUGUE interface was adding wrong parameter in forward warping mode.
 * API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 0d82b258ba..0592948017 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -678,17 +678,17 @@ def _list_outputs(self):
                                                       '_variance.ext', cwd=cwd)
             outputs['std_img'] = self._gen_fname(outputs['out_file'] +
                                                  '_sigma.ext', cwd=cwd)
-                                                  
+
         # The mean image created if -stats option is specified ('meanvol')
-        # is missing the top and bottom slices. Therefore we only expose the 
-        # mean image created by -meanvol option ('mean_reg') which isn't 
+        # is missing the top and bottom slices. Therefore we only expose the
+        # mean image created by -meanvol option ('mean_reg') which isn't
         # corrupted.
         # Note that the same problem holds for the std and variance image.
-                                                  
+
         if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
             outputs['mean_img'] = self._gen_fname(outputs['out_file'] +
                                                   '_mean_reg.ext', cwd=cwd)
-                                                  
+
         if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
             _, filename = os.path.split(outputs['out_file'])
             matpathname = os.path.join(cwd, filename + '.mat')
@@ -1159,9 +1159,8 @@ def _gen_filename(self, name):
 class FUGUEInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
                    desc='filename of input volume')
-    unwarped_file = File(
-        argstr='--unwarp=%s', genfile=True,
-        desc='apply unwarping and save as filename', hash_files=False)
+    unwarped_file = File(argstr='--unwarp=%s', desc='apply unwarping and save as filename',
+                         hash_files=False)
     forward_warping = traits.Bool(
         False, usedefault=True,
         desc='apply forward warping instead of unwarping')
@@ -1242,7 +1241,16 @@ class FUGUE(FSLCommand):
     Examples
     --------
 
-    Please insert examples for use of this command
+    >>> from nipype.interfaces.fsl.preprocess import FUGUE
+    >>> fugue = FUGUE()
+    >>> fugue.inputs.forward_warping = True
+    >>> fugue.inputs.in_file = 'epi.nii'
+    >>> fugue.inputs.mask_file = 'epi_mask.nii'
+    >>> fugue.inputs.shift_in_file = 'image.nii'  # Previously computed with fugue as well
+    >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.cmdline #doctest: +ELLIPSIS
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=image.nii --unwarpdir=y --warp=.../epi_warped.nii.gz'
+    >>> fugue.run() #doctest: +SKIP
 
     """
 
@@ -1257,10 +1265,14 @@ def __init__(self, **kwargs):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        if self.inputs.forward_warping:
+
+        if isdefined(self.inputs.forward_warping) and self.inputs.forward_warping:
             out_field = 'warped_file'
+            self.inputs.unwarped_file = Undefined
+            outputs.pop('unwarped_file')
         else:
             out_field = 'unwarped_file'
+            outputs.pop('warped_file')
 
         out_file = getattr(self.inputs, out_field)
         if not isdefined(out_file):
@@ -1279,10 +1291,11 @@ def _list_outputs(self):
         return outputs
 
     def _gen_filename(self, name):
-        if name == 'unwarped_file' and not self.inputs.forward_warping:
-            return self._list_outputs()['unwarped_file']
-        if name == 'warped_file' and self.inputs.forward_warping:
-            return self._list_outputs()['warped_file']
+        is_fwd = isdefined(self.inputs.forward_warping) and self.inputs.forward_warping
+
+        if (is_fwd and name=='warped_file') or (not is_fwd and name=='unwarped_file'):
+            return self._list_outputs()[name]
+
         return None
 
     def _parse_inputs(self, skip=None):
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index d27a0f9d27..4de0f52fcf 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -79,7 +79,6 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
-    genfile=True,
     hash_files=False,
     ),
     warped_file=dict(argstr='--warp=%s',

From 4ae194f79ddd95a0b6fef806940a67b456f5662a Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 11 Jun 2014 13:18:33 +0200
Subject: [PATCH 02/11] Fix incorrect requirement of FUGUE input

---
 nipype/interfaces/fsl/preprocess.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 0d82b258ba..4cbd3220c7 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -678,17 +678,17 @@ def _list_outputs(self):
                                                       '_variance.ext', cwd=cwd)
             outputs['std_img'] = self._gen_fname(outputs['out_file'] +
                                                  '_sigma.ext', cwd=cwd)
-                                                  
+
         # The mean image created if -stats option is specified ('meanvol')
-        # is missing the top and bottom slices. Therefore we only expose the 
-        # mean image created by -meanvol option ('mean_reg') which isn't 
+        # is missing the top and bottom slices. Therefore we only expose the
+        # mean image created by -meanvol option ('mean_reg') which isn't
         # corrupted.
         # Note that the same problem holds for the std and variance image.
-                                                  
+
         if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
             outputs['mean_img'] = self._gen_fname(outputs['out_file'] +
                                                   '_mean_reg.ext', cwd=cwd)
-                                                  
+
         if isdefined(self.inputs.save_mats) and self.inputs.save_mats:
             _, filename = os.path.split(outputs['out_file'])
             matpathname = os.path.join(cwd, filename + '.mat')
@@ -1223,7 +1223,7 @@ class FUGUEInputSpec(FSLCommandInputSpec):
                                      requires=['fmap_out_file'],
                                      desc='saves the unmasked fieldmap when using --savefmap')
     save_unmasked_shift = traits.Bool(argstr='--unmaskshift',
-                                      requires=['shift_out_file'],
+                                      requires=['save_shift'],
                                       desc='saves the unmasked shiftmap when using --saveshift')
     nokspace = traits.Bool(
         argstr='--nokspace', desc='do not use k-space forward warping')

From 0998e5e6bfb049adf8754972e02c5dbb19d44b3d Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 11 Jun 2014 15:23:32 +0200
Subject: [PATCH 03/11] Run make specs to fix auto test

---
 nipype/interfaces/fsl/tests/test_auto_FUGUE.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index d27a0f9d27..977a49186c 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -62,7 +62,7 @@ def test_FUGUE_inputs():
     requires=['fmap_out_file'],
     ),
     save_unmasked_shift=dict(argstr='--unmaskshift',
-    requires=['shift_out_file'],
+    requires=['save_shift'],
     ),
     shift_in_file=dict(argstr='--loadshift=%s',
     ),

From d9f3442c3036e1f50fb7be886407614581ed715d Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 4 Jul 2014 11:51:52 +0200
Subject: [PATCH 04/11] FUGUE interface refactored.

Deeply reviewed the interface to use the new name_template system,
along with the correction of several issues. Also includes changes
of another PR, so close #856.
---
 nipype/interfaces/fsl/preprocess.py           | 207 ++++++++++--------
 .../interfaces/fsl/tests/test_auto_FUGUE.py   |  16 +-
 nipype/testing/data/epi_phasediff.nii         |   0
 nipype/testing/data/vsm.nii                   |   0
 4 files changed, 128 insertions(+), 95 deletions(-)
 create mode 100644 nipype/testing/data/epi_phasediff.nii
 create mode 100644 nipype/testing/data/vsm.nii

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 3339b07f80..40d84b2d20 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1159,34 +1159,27 @@ def _gen_filename(self, name):
 class FUGUEInputSpec(FSLCommandInputSpec):
     in_file = File(exists=True, argstr='--in=%s',
                    desc='filename of input volume')
+    shift_in_file = File(exists=True, argstr='--loadshift=%s',
+                         desc='filename for reading pixel shift volume')
+    phasemap_in_file = File(exists=True, argstr='--phasemap=%s',
+                            desc='filename for input phase image')
+    fmap_in_file = File(exists=True, argstr='--loadfmap=%s',
+                        desc='filename for loading fieldmap (rad/s)')
     unwarped_file = File(argstr='--unwarp=%s', desc='apply unwarping and save as filename',
-                         hash_files=False)
-    forward_warping = traits.Bool(
-        False, usedefault=True,
-        desc='apply forward warping instead of unwarping')
-    warped_file = File(argstr='--warp=%s',
-                       desc='apply forward warping and save as filename',
-                       hash_files=False)
-    phasemap_file = File(exists=True, argstr='--phasemap=%s',
-                         desc='filename for input phase image')
+                         xor=['warped_file'])
+    warped_file = File(argstr='--warp=%s', desc='apply forward warping and save as filename',
+                       xor=['unwarped_file'])
+
+    forward_warping = traits.Bool(False, usedefault=True, mandatory=True,
+                                  desc='apply forward warping instead of unwarping')
+
     dwell_to_asym_ratio = traits.Float(argstr='--dwelltoasym=%.10f',
                                        desc='set the dwell to asym time ratio')
     dwell_time = traits.Float(argstr='--dwell=%.10f',
-                              desc='set the EPI dwell time per phase-encode line - same as echo spacing - (sec)')
+                              desc=('set the EPI dwell time per phase-encode line - same as echo '
+                                    'spacing - (sec)'))
     asym_se_time = traits.Float(argstr='--asym=%.10f',
                                 desc='set the fieldmap asymmetric spin echo time (sec)')
-    fmap_out_file = File(argstr='--savefmap=%s',
-                     desc='filename for saving fieldmap (rad/s)', hash_files=False)
-    fmap_in_file = File(exists=True, argstr='--loadfmap=%s',
-                        desc='filename for loading fieldmap (rad/s)')
-
-    save_shift = traits.Bool(desc='output pixel shift volume')
-
-    shift_out_file = traits.File(argstr='--saveshift=%s',
-                           desc='filename for saving pixel shift volume', hash_files=False)
-
-    shift_in_file = File(exists=True, argstr='--loadshift=%s',
-                         desc='filename for reading pixel shift volume')
     median_2dfilter = traits.Bool(argstr='--median',
                                 desc='apply 2D median filtering')
     despike_2dfilter = traits.Bool(argstr='--despike',
@@ -1216,16 +1209,22 @@ class FUGUEInputSpec(FSLCommandInputSpec):
                         desc='apply intensity correction to unwarping (pixel shift method only)')
     icorr_only = traits.Bool(argstr='--icorronly', requires=['unwarped_file'],
                              desc='apply intensity correction only')
-    mask_file = File(exists=True, argstr='--mask=%s',
-                     desc='filename for loading valid mask')
-    save_unmasked_fmap = traits.Bool(argstr='--unmaskfmap',
-                                     requires=['fmap_out_file'],
-                                     desc='saves the unmasked fieldmap when using --savefmap')
-    save_unmasked_shift = traits.Bool(argstr='--unmaskshift',
-                                      requires=['save_shift'],
+    mask_file = File(exists=True, argstr='--mask=%s', desc='filename for loading valid mask')
+    nokspace = traits.Bool(False, argstr='--nokspace', desc='do not use k-space forward warping')
+
+    # Special outputs: shift (voxel shift map, vsm)
+    save_shift = traits.Bool(False, desc='write pixel shift volume')
+    shift_out_file = File(argstr='--saveshift=%s', desc='filename for saving pixel shift volume')
+    save_unmasked_shift = traits.Bool(argstr='--unmaskshift', xor=['save_shift'],
                                       desc='saves the unmasked shiftmap when using --saveshift')
-    nokspace = traits.Bool(
-        argstr='--nokspace', desc='do not use k-space forward warping')
+
+    # Special outputs: fieldmap (fmap)
+    save_fmap = traits.Bool(False, desc='write field map volume')
+    fmap_out_file = File(argstr='--savefmap=%s', desc='filename for saving fieldmap (rad/s)')
+    save_unmasked_fmap = traits.Bool(False, argstr='--unmaskfmap', xor=['save_fmap'],
+                                     desc='saves the unmasked fieldmap when using --savefmap')
+
+
 
 
 class FUGUEOutputSpec(TraitedSpec):
@@ -1238,87 +1237,121 @@ class FUGUEOutputSpec(TraitedSpec):
 class FUGUE(FSLCommand):
     """Use FSL FUGUE to unwarp epi's with fieldmaps
 
-    Examples
-    --------
+    Example (unwarping an input image, the shift map is known) ::
 
     >>> from nipype.interfaces.fsl.preprocess import FUGUE
     >>> fugue = FUGUE()
-    >>> fugue.inputs.forward_warping = True
     >>> fugue.inputs.in_file = 'epi.nii'
     >>> fugue.inputs.mask_file = 'epi_mask.nii'
-    >>> fugue.inputs.shift_in_file = 'image.nii'  # Previously computed with fugue as well
+    >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.cmdline #doctest: +ELLIPSIS
-    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=image.nii --unwarpdir=y --warp=.../epi_warped.nii.gz'
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=.../epi_unwarped.nii.gz'
     >>> fugue.run() #doctest: +SKIP
 
-    """
 
-    _cmd = 'fugue'
-    input_spec = FUGUEInputSpec
-    output_spec = FUGUEOutputSpec
+    Example (warping an input image, shift map is known) ::
 
-    def __init__(self, **kwargs):
-        super(FUGUE, self).__init__(**kwargs)
-        warn(
-            'This interface has not been fully tested. Please report any failures.')
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
+    >>> from nipype.interfaces.fsl.preprocess import FUGUE
+    >>> fugue = FUGUE()
+    >>> fugue.inputs.forward_warping = True
+    >>> fugue.inputs.in_file = 'epi.nii'
+    >>> fugue.inputs.mask_file = 'epi_mask.nii'
+    >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
+    >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.cmdline #doctest: +ELLIPSIS
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=.../epi_warped.nii.gz'
+    >>> fugue.run() #doctest: +SKIP
 
-        if isdefined(self.inputs.forward_warping) and self.inputs.forward_warping:
-            out_field = 'warped_file'
-            self.inputs.unwarped_file = Undefined
-            outputs.pop('unwarped_file')
-        else:
-            out_field = 'unwarped_file'
-            outputs.pop('warped_file')
 
-        out_file = getattr(self.inputs, out_field)
-        if not isdefined(out_file):
-            if isdefined(self.inputs.in_file):
-                out_file = self._gen_fname(self.inputs.in_file,
-                                           suffix='_'+out_field[:-5])
-        if isdefined(out_file):
-            outputs[out_field] = os.path.abspath(out_file)
-        if isdefined(self.inputs.fmap_out_file):
-            outputs['fmap_out_file'] = os.path.abspath(
-                self.inputs.fmap_out_file)
-        if isdefined(self.inputs.shift_out_file):
-            outputs['shift_out_file'] = os.path.abspath(
-                self.inputs.shift_out_file)
+    Example (computing the vsm, unwrapped phase map is known) ::
 
-        return outputs
+    >>> from nipype.interfaces.fsl.preprocess import FUGUE
+    >>> fugue = FUGUE()
+    >>> fugue.inputs.phasemap_in_file = 'epi_phasediff.nii'
+    >>> fugue.inputs.mask_file = 'epi_mask.nii'
+    >>> fugue.inputs.dwell_to_asym_ratio = 0.77e-3 / 2.46e-3
+    >>> fugue.inputs.unwarp_direction = 'y'
+    >>> fugue.inputs.save_shift = True
+    >>> fugue.cmdline #doctest: +ELLIPSIS
+    'fugue --dwelltoasym=0.7000000000 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=.../epi_phasediff_vsm.nii.gz --unwarpdir=y'
+    >>> fugue.run() #doctest: +SKIP
 
-    def _gen_filename(self, name):
-        is_fwd = isdefined(self.inputs.forward_warping) and self.inputs.forward_warping
 
-        if (is_fwd and name=='warped_file') or (not is_fwd and name=='unwarped_file'):
-            return self._list_outputs()[name]
+    """
 
-        return None
+    _cmd = 'fugue'
+    input_spec = FUGUEInputSpec
+    output_spec = FUGUEOutputSpec
 
     def _parse_inputs(self, skip=None):
         if skip is None:
             skip = []
 
-        if not isdefined(self.inputs.save_shift) or not self.inputs.save_shift:
-            skip += ['shift_out_file']
-        else:
-            if not isdefined(self.inputs.shift_out_file):
-                self.inputs.shift_out_file = self._gen_fname(
-                    self.inputs.in_file, suffix='_vsm')
+        input_phase = isdefined(self.inputs.phasemap_in_file)
+        input_vsm = isdefined(self.inputs.shift_in_file)
+        input_fmap = isdefined(self.inputs.fmap_in_file)
+
+        if not input_phase and not input_vsm and not input_fmap:
+            raise RuntimeError('Either phasemap_in_file, shift_in_file or fmap_in_file must be set.')
 
         if not isdefined(self.inputs.in_file):
             skip += ['unwarped_file', 'warped_file']
-        elif self.inputs.forward_warping:
-            if not isdefined(self.inputs.warped_file):
-                self.inputs.warped_file = self._gen_fname(
-                    self.inputs.in_file, suffix='_warped')
-        elif not self.inputs.forward_warping:
-            if not isdefined(self.inputs.unwarped_file):
-                self.inputs.unwarped_file = self._gen_fname(
-                    self.inputs.in_file, suffix='_unwarped')
+        else:
+            if self.inputs.forward_warping:
+                skip += ['unwarped_file']
+                trait_spec = self.inputs.trait('warped_file')
+                trait_spec.name_template = "%s_warped"
+                trait_spec.name_source = ['in_file']
+                trait_spec.output_name = 'warped_file'
+            else:
+                skip += ['warped_file']
+                trait_spec = self.inputs.trait('unwarped_file')
+                trait_spec.name_template = "%s_unwarped"
+                trait_spec.name_source = ['in_file']
+                trait_spec.output_name = 'unwarped_file'
+
+        # Handle shift output
+        vsm_save_masked = isdefined(self.inputs.save_shift) and self.inputs.save_shift
+        vsm_save_unmasked = isdefined(self.inputs.save_unmasked_shift) \
+                            and self.inputs.save_unmasked_shift
+
+        if (vsm_save_masked or vsm_save_unmasked) and not isdefined(self.inputs.shift_out_file):
+            trait_spec = self.inputs.trait('shift_out_file')
+            trait_spec.output_name = 'shift_out_file'
+
+            if vsm_save_unmasked:
+                trait_spec.name_template = '%s_vsm_unmasked'
+            else:
+                trait_spec.name_template = '%s_vsm'
+
+            if input_fmap:
+                trait_spec.name_source = ['fmap_in_file']
+            elif input_phase:
+                trait_spec.name_source = ['phasemap_in_file']
+            else:
+                trait_spec.name_source = ['shift_in_file']
+
+        # Handle fieldmap output
+        fmap_save_masked = isdefined(self.inputs.save_fmap) and self.inputs.save_shift
+        fmap_save_unmasked = isdefined(self.inputs.save_unmasked_fmap) and \
+                             self.inputs.save_unmasked_fmap
+
+        if (fmap_save_masked or fmap_save_unmasked) and not isdefined(self.inputs.fmap_out_file):
+            trait_spec = self.inputs.trait('fmap_out_file')
+            trait_spec.output_name = 'fmap_out_file'
+
+            if fmap_save_unmasked:
+                trait_spec.name_template = '%s_fieldmap_unmasked'
+            else:
+                trait_spec.name_template = '%s_fieldmap'
+
+            if input_vsm:
+                trait_spec.name_source = ['shift_in_file']
+            elif input_phase:
+                trait_spec.name_source = ['phasemap_in_file']
+            else:
+                trait_spec.name_source = ['fmap_in_file']
 
         return super(FUGUE, self)._parse_inputs(skip=skip)
 
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index 38754d9162..28d747d4a1 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -21,9 +21,9 @@ def test_FUGUE_inputs():
     fmap_in_file=dict(argstr='--loadfmap=%s',
     ),
     fmap_out_file=dict(argstr='--savefmap=%s',
-    hash_files=False,
     ),
-    forward_warping=dict(usedefault=True,
+    forward_warping=dict(mandatory=True,
+    usedefault=True,
     ),
     fourier_order=dict(argstr='--fourier=%d',
     ),
@@ -53,21 +53,21 @@ def test_FUGUE_inputs():
     ),
     phase_conjugate=dict(argstr='--phaseconj',
     ),
-    phasemap_file=dict(argstr='--phasemap=%s',
+    phasemap_in_file=dict(argstr='--phasemap=%s',
     ),
     poly_order=dict(argstr='--poly=%d',
     ),
+    save_fmap=dict(),
     save_shift=dict(),
     save_unmasked_fmap=dict(argstr='--unmaskfmap',
-    requires=['fmap_out_file'],
+    xor=['save_fmap'],
     ),
     save_unmasked_shift=dict(argstr='--unmaskshift',
-    requires=['save_shift'],
+    xor=['save_shift'],
     ),
     shift_in_file=dict(argstr='--loadshift=%s',
     ),
     shift_out_file=dict(argstr='--saveshift=%s',
-    hash_files=False,
     ),
     smooth2d=dict(argstr='--smooth2=%.2f',
     ),
@@ -79,10 +79,10 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
-    hash_files=False,
+    xor=['warped_file'],
     ),
     warped_file=dict(argstr='--warp=%s',
-    hash_files=False,
+    xor=['unwarped_file'],
     ),
     )
     inputs = FUGUE.input_spec()
diff --git a/nipype/testing/data/epi_phasediff.nii b/nipype/testing/data/epi_phasediff.nii
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/nipype/testing/data/vsm.nii b/nipype/testing/data/vsm.nii
new file mode 100644
index 0000000000..e69de29bb2

From d24c5cd33e30ee777a5625681d12f03495318195 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 4 Jul 2014 12:07:59 +0200
Subject: [PATCH 05/11] Fixed doctests. Fixed fsl.epi workflow.

The workflow was using an input with its name changed.
---
 CHANGES                             |  2 +-
 nipype/interfaces/fsl/preprocess.py | 29 +++++++++++++++++++++--------
 nipype/workflows/dmri/fsl/epi.py    |  4 ++--
 3 files changed, 24 insertions(+), 11 deletions(-)

diff --git a/CHANGES b/CHANGES
index 4fb242cb24..573fc27183 100644
--- a/CHANGES
+++ b/CHANGES
@@ -1,7 +1,7 @@
 Next Release
 ============
 
-* FIX: FUGUE interface was adding wrong parameter in forward warping mode.
+* ENH: FUGUE interface has been refactored to use the name_template system, 3 examples added to doctests, some bugs solved.
 * API: Interfaces to external packages are no longer available in the top-level ``nipype`` namespace, and must be imported directly (e.g. ``from nipype.interfaces import fsl``).
 * ENH: New ANTs interface: ApplyTransformsToPoints
 * ENH: New FreeSurfer workflow: create_skullstripped_recon_flow()
diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 40d84b2d20..627ea96b71 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1235,9 +1235,22 @@ class FUGUEOutputSpec(TraitedSpec):
 
 
 class FUGUE(FSLCommand):
-    """Use FSL FUGUE to unwarp epi's with fieldmaps
+    """
+    `FUGUE <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FUGUE>`_ is, most generally, a set of tools for
+    EPI distortion correction.
+
+    Distortions may be corrected for
+        1. improving registration with non-distorted images (e.g. structurals), or
+        2. dealing with motion-dependent changes.
+
+    FUGUE is designed to deal only with the first case - improving registration.
+
+
+    Examples
+    --------
+
 
-    Example (unwarping an input image, the shift map is known) ::
+    Unwarping an input image (shift map is known) ::
 
     >>> from nipype.interfaces.fsl.preprocess import FUGUE
     >>> fugue = FUGUE()
@@ -1246,11 +1259,11 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.cmdline #doctest: +ELLIPSIS
-    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=.../epi_unwarped.nii.gz'
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz'
     >>> fugue.run() #doctest: +SKIP
 
 
-    Example (warping an input image, shift map is known) ::
+    Warping an input image (shift map is known) ::
 
     >>> from nipype.interfaces.fsl.preprocess import FUGUE
     >>> fugue = FUGUE()
@@ -1260,21 +1273,21 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.cmdline #doctest: +ELLIPSIS
-    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=.../epi_warped.nii.gz'
+    'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz'
     >>> fugue.run() #doctest: +SKIP
 
 
-    Example (computing the vsm, unwrapped phase map is known) ::
+    Computing the vsm (unwrapped phase map is known) ::
 
     >>> from nipype.interfaces.fsl.preprocess import FUGUE
     >>> fugue = FUGUE()
     >>> fugue.inputs.phasemap_in_file = 'epi_phasediff.nii'
     >>> fugue.inputs.mask_file = 'epi_mask.nii'
-    >>> fugue.inputs.dwell_to_asym_ratio = 0.77e-3 / 2.46e-3
+    >>> fugue.inputs.dwell_to_asym_ratio = (0.77e-3 * 3) / 2.46e-3
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.inputs.save_shift = True
     >>> fugue.cmdline #doctest: +ELLIPSIS
-    'fugue --dwelltoasym=0.7000000000 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=.../epi_phasediff_vsm.nii.gz --unwarpdir=y'
+    'fugue --dwelltoasym=0.3130081301 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
     >>> fugue.run() #doctest: +SKIP
 
 
diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py
index 194b62c9e0..48fb6e8b32 100644
--- a/nipype/workflows/dmri/fsl/epi.py
+++ b/nipype/workflows/dmri/fsl/epi.py
@@ -337,7 +337,7 @@ def fieldmap_correction(name='fieldmap_correction', nocheck=False):
                     ,(inputnode,      mask_mag, [('in_mask', 'mask_file' )])
                     ,(select_mag,     mask_mag, [('roi_file', 'in_file')])
                     ,(mask_mag,        fslprep, [('out_file', 'in_magnitude')])
-                    ,(fslprep,             vsm, [('out_fieldmap', 'phasemap_file')])
+                    ,(fslprep,             vsm, [('out_fieldmap', 'phasemap_in_file')])
                     ,(inputnode,           vsm, [('fieldmap_mag', 'in_file'),
                                                  ('encoding_direction','unwarp_direction'),
                                                  (('te_diff', _ms2sec), 'asym_se_time'),
@@ -550,7 +550,7 @@ def create_epidewarp_pipeline(name='epidewarp', fieldmap_registration=False):
                     ,(mask_mag_dil,    prelude, [('out_file', 'mask_file')])
                     ,(prelude,      fill_phase, [('unwrapped_phase_file', 'in_file')])
                     ,(inputnode,           vsm, [('fieldmap_mag', 'in_file')])
-                    ,(fill_phase,          vsm, [('out_file', 'phasemap_file')])
+                    ,(fill_phase,          vsm, [('out_file', 'phasemap_in_file')])
                     ,(inputnode,           vsm, [(('te_diff', _ms2sec), 'asym_se_time'), ('vsm_sigma', 'smooth2d')])
                     ,(dwell_time,          vsm, [(('dwell_time', _ms2sec), 'dwell_time')])
                     ,(mask_mag_dil,        vsm, [('out_file', 'mask_file')])

From 3a8257808a2268260509404fbb7500f9bfb7b317 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Fri, 4 Jul 2014 12:17:35 +0200
Subject: [PATCH 06/11] Fixed doctest

---
 nipype/interfaces/fsl/preprocess.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 627ea96b71..fe55382a65 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1287,7 +1287,7 @@ class FUGUE(FSLCommand):
     >>> fugue.inputs.unwarp_direction = 'y'
     >>> fugue.inputs.save_shift = True
     >>> fugue.cmdline #doctest: +ELLIPSIS
-    'fugue --dwelltoasym=0.3130081301 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
+    'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y'
     >>> fugue.run() #doctest: +SKIP
 
 

From d577f5db6f23ac3a09601b233b65683e722f3b0d Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 7 Jul 2014 15:42:23 +0200
Subject: [PATCH 07/11] Added requirements of interface.

Also replaced the name_source dynamic setting with str instead of lists,
as it seems to produce errors when executing as MapNode of workflows.
---
 nipype/interfaces/fsl/preprocess.py           | 22 +++++++++----------
 .../interfaces/fsl/tests/test_auto_FUGUE.py   |  3 +++
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index fe55382a65..1e93e278aa 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1166,11 +1166,11 @@ class FUGUEInputSpec(FSLCommandInputSpec):
     fmap_in_file = File(exists=True, argstr='--loadfmap=%s',
                         desc='filename for loading fieldmap (rad/s)')
     unwarped_file = File(argstr='--unwarp=%s', desc='apply unwarping and save as filename',
-                         xor=['warped_file'])
+                         xor=['warped_file'], requires=['in_file'])
     warped_file = File(argstr='--warp=%s', desc='apply forward warping and save as filename',
-                       xor=['unwarped_file'])
+                       xor=['unwarped_file'], requires=['in_file'])
 
-    forward_warping = traits.Bool(False, usedefault=True, mandatory=True,
+    forward_warping = traits.Bool(False, usedefault=True, mandatory=True, requires=['in_file'],
                                   desc='apply forward warping instead of unwarping')
 
     dwell_to_asym_ratio = traits.Float(argstr='--dwelltoasym=%.10f',
@@ -1315,13 +1315,13 @@ def _parse_inputs(self, skip=None):
                 skip += ['unwarped_file']
                 trait_spec = self.inputs.trait('warped_file')
                 trait_spec.name_template = "%s_warped"
-                trait_spec.name_source = ['in_file']
+                trait_spec.name_source = 'in_file'
                 trait_spec.output_name = 'warped_file'
             else:
                 skip += ['warped_file']
                 trait_spec = self.inputs.trait('unwarped_file')
                 trait_spec.name_template = "%s_unwarped"
-                trait_spec.name_source = ['in_file']
+                trait_spec.name_source = 'in_file'
                 trait_spec.output_name = 'unwarped_file'
 
         # Handle shift output
@@ -1339,11 +1339,11 @@ def _parse_inputs(self, skip=None):
                 trait_spec.name_template = '%s_vsm'
 
             if input_fmap:
-                trait_spec.name_source = ['fmap_in_file']
+                trait_spec.name_source = 'fmap_in_file'
             elif input_phase:
-                trait_spec.name_source = ['phasemap_in_file']
+                trait_spec.name_source = 'phasemap_in_file'
             else:
-                trait_spec.name_source = ['shift_in_file']
+                trait_spec.name_source = 'shift_in_file'
 
         # Handle fieldmap output
         fmap_save_masked = isdefined(self.inputs.save_fmap) and self.inputs.save_shift
@@ -1360,11 +1360,11 @@ def _parse_inputs(self, skip=None):
                 trait_spec.name_template = '%s_fieldmap'
 
             if input_vsm:
-                trait_spec.name_source = ['shift_in_file']
+                trait_spec.name_source = 'shift_in_file'
             elif input_phase:
-                trait_spec.name_source = ['phasemap_in_file']
+                trait_spec.name_source = 'phasemap_in_file'
             else:
-                trait_spec.name_source = ['fmap_in_file']
+                trait_spec.name_source = 'fmap_in_file'
 
         return super(FUGUE, self)._parse_inputs(skip=skip)
 
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index 28d747d4a1..5b3f1f2831 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -23,6 +23,7 @@ def test_FUGUE_inputs():
     fmap_out_file=dict(argstr='--savefmap=%s',
     ),
     forward_warping=dict(mandatory=True,
+    requires=['in_file'],
     usedefault=True,
     ),
     fourier_order=dict(argstr='--fourier=%d',
@@ -79,9 +80,11 @@ def test_FUGUE_inputs():
     unwarp_direction=dict(argstr='--unwarpdir=%s',
     ),
     unwarped_file=dict(argstr='--unwarp=%s',
+    requires=['in_file'],
     xor=['warped_file'],
     ),
     warped_file=dict(argstr='--warp=%s',
+    requires=['in_file'],
     xor=['unwarped_file'],
     ),
     )

From cd329a4d75effb50cf1c020dc9881805aa47ec5a Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 7 Jul 2014 16:10:31 +0200
Subject: [PATCH 08/11] Removed requires as it breaks doctests

---
 nipype/interfaces/fsl/preprocess.py            | 4 ++--
 nipype/interfaces/fsl/tests/test_auto_FUGUE.py | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 1e93e278aa..598aa3334f 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1170,7 +1170,7 @@ class FUGUEInputSpec(FSLCommandInputSpec):
     warped_file = File(argstr='--warp=%s', desc='apply forward warping and save as filename',
                        xor=['unwarped_file'], requires=['in_file'])
 
-    forward_warping = traits.Bool(False, usedefault=True, mandatory=True, requires=['in_file'],
+    forward_warping = traits.Bool(False, usedefault=True,
                                   desc='apply forward warping instead of unwarping')
 
     dwell_to_asym_ratio = traits.Float(argstr='--dwelltoasym=%.10f',
@@ -1267,8 +1267,8 @@ class FUGUE(FSLCommand):
 
     >>> from nipype.interfaces.fsl.preprocess import FUGUE
     >>> fugue = FUGUE()
-    >>> fugue.inputs.forward_warping = True
     >>> fugue.inputs.in_file = 'epi.nii'
+    >>> fugue.inputs.forward_warping = True
     >>> fugue.inputs.mask_file = 'epi_mask.nii'
     >>> fugue.inputs.shift_in_file = 'vsm.nii'  # Previously computed with fugue as well
     >>> fugue.inputs.unwarp_direction = 'y'
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index 5b3f1f2831..e1bcbadfa5 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -22,9 +22,7 @@ def test_FUGUE_inputs():
     ),
     fmap_out_file=dict(argstr='--savefmap=%s',
     ),
-    forward_warping=dict(mandatory=True,
-    requires=['in_file'],
-    usedefault=True,
+    forward_warping=dict(usedefault=True,
     ),
     fourier_order=dict(argstr='--fourier=%d',
     ),

From f0838959b4fe8a991a75cb657572fb4fb7435113 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 8 Jul 2014 11:34:10 +0200
Subject: [PATCH 09/11] Fixed some (too) long logical statements to agree with
 PEP8

---
 nipype/interfaces/fsl/preprocess.py           | 58 +++++++++++--------
 .../interfaces/fsl/tests/test_auto_FUGUE.py   |  6 +-
 2 files changed, 39 insertions(+), 25 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 598aa3334f..0822c11949 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1213,13 +1213,15 @@ class FUGUEInputSpec(FSLCommandInputSpec):
     nokspace = traits.Bool(False, argstr='--nokspace', desc='do not use k-space forward warping')
 
     # Special outputs: shift (voxel shift map, vsm)
-    save_shift = traits.Bool(False, desc='write pixel shift volume')
+    save_shift = traits.Bool(False, xor=['save_unmasked_shift'],
+                             desc='write pixel shift volume')
     shift_out_file = File(argstr='--saveshift=%s', desc='filename for saving pixel shift volume')
     save_unmasked_shift = traits.Bool(argstr='--unmaskshift', xor=['save_shift'],
                                       desc='saves the unmasked shiftmap when using --saveshift')
 
     # Special outputs: fieldmap (fmap)
-    save_fmap = traits.Bool(False, desc='write field map volume')
+    save_fmap = traits.Bool(False, xor=['save_unmasked_fmap'],
+                            desc='write field map volume')
     fmap_out_file = File(argstr='--savefmap=%s', desc='filename for saving fieldmap (rad/s)')
     save_unmasked_fmap = traits.Bool(False, argstr='--unmaskfmap', xor=['save_fmap'],
                                      desc='saves the unmasked fieldmap when using --savefmap')
@@ -1325,46 +1327,56 @@ def _parse_inputs(self, skip=None):
                 trait_spec.output_name = 'unwarped_file'
 
         # Handle shift output
-        vsm_save_masked = isdefined(self.inputs.save_shift) and self.inputs.save_shift
-        vsm_save_unmasked = isdefined(self.inputs.save_unmasked_shift) \
-                            and self.inputs.save_unmasked_shift
+        vsm_save_masked = (isdefined(self.inputs.save_shift) and self.inputs.save_shift)
+        vsm_save_unmasked = (isdefined(self.inputs.save_unmasked_shift) and
+                             self.inputs.save_unmasked_shift)
 
-        if (vsm_save_masked or vsm_save_unmasked) and not isdefined(self.inputs.shift_out_file):
+        if ((vsm_save_masked or vsm_save_unmasked) and
+            not isdefined(self.inputs.shift_out_file)):
             trait_spec = self.inputs.trait('shift_out_file')
-            trait_spec.output_name = 'shift_out_file'
-
-            if vsm_save_unmasked:
-                trait_spec.name_template = '%s_vsm_unmasked'
-            else:
-                trait_spec.name_template = '%s_vsm'
 
             if input_fmap:
                 trait_spec.name_source = 'fmap_in_file'
             elif input_phase:
                 trait_spec.name_source = 'phasemap_in_file'
-            else:
+            elif input_vsm:
                 trait_spec.name_source = 'shift_in_file'
+            else:
+                raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
+                                   'fmap_in_file must be set.'))
+
+            trait_spec.output_name = 'shift_out_file'
+
+            if vsm_save_unmasked:
+                trait_spec.name_template = '%s_vsm_unmasked'
+            else:
+                trait_spec.name_template = '%s_vsm'
 
         # Handle fieldmap output
         fmap_save_masked = isdefined(self.inputs.save_fmap) and self.inputs.save_shift
-        fmap_save_unmasked = isdefined(self.inputs.save_unmasked_fmap) and \
-                             self.inputs.save_unmasked_fmap
+        fmap_save_unmasked = (isdefined(self.inputs.save_unmasked_fmap) and
+                              self.inputs.save_unmasked_fmap)
 
-        if (fmap_save_masked or fmap_save_unmasked) and not isdefined(self.inputs.fmap_out_file):
+        if ((fmap_save_masked or fmap_save_unmasked) and
+            not isdefined(self.inputs.fmap_out_file)):
             trait_spec = self.inputs.trait('fmap_out_file')
-            trait_spec.output_name = 'fmap_out_file'
-
-            if fmap_save_unmasked:
-                trait_spec.name_template = '%s_fieldmap_unmasked'
-            else:
-                trait_spec.name_template = '%s_fieldmap'
 
             if input_vsm:
                 trait_spec.name_source = 'shift_in_file'
             elif input_phase:
                 trait_spec.name_source = 'phasemap_in_file'
-            else:
+            elif input_fmap:
                 trait_spec.name_source = 'fmap_in_file'
+            else:
+                raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
+                                   'fmap_in_file must be set.'))
+
+            trait_spec.output_name = 'fmap_out_file'
+
+            if fmap_save_unmasked:
+                trait_spec.name_template = '%s_fieldmap_unmasked'
+            else:
+                trait_spec.name_template = '%s_fieldmap'
 
         return super(FUGUE, self)._parse_inputs(skip=skip)
 
diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
index e1bcbadfa5..918e80c519 100644
--- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
+++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py
@@ -56,8 +56,10 @@ def test_FUGUE_inputs():
     ),
     poly_order=dict(argstr='--poly=%d',
     ),
-    save_fmap=dict(),
-    save_shift=dict(),
+    save_fmap=dict(xor=['save_unmasked_fmap'],
+    ),
+    save_shift=dict(xor=['save_unmasked_shift'],
+    ),
     save_unmasked_fmap=dict(argstr='--unmaskfmap',
     xor=['save_fmap'],
     ),

From 53bc39588b7acffa13f6192e318e3646ed727259 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 8 Jul 2014 11:54:15 +0200
Subject: [PATCH 10/11] Still having problems when running fugue inside a
 mapnode

---
 nipype/interfaces/fsl/preprocess.py | 92 +++++++++++++++--------------
 1 file changed, 48 insertions(+), 44 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 0822c11949..21ac7940e7 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1327,56 +1327,60 @@ def _parse_inputs(self, skip=None):
                 trait_spec.output_name = 'unwarped_file'
 
         # Handle shift output
-        vsm_save_masked = (isdefined(self.inputs.save_shift) and self.inputs.save_shift)
-        vsm_save_unmasked = (isdefined(self.inputs.save_unmasked_shift) and
-                             self.inputs.save_unmasked_shift)
-
-        if ((vsm_save_masked or vsm_save_unmasked) and
-            not isdefined(self.inputs.shift_out_file)):
-            trait_spec = self.inputs.trait('shift_out_file')
-
-            if input_fmap:
-                trait_spec.name_source = 'fmap_in_file'
-            elif input_phase:
-                trait_spec.name_source = 'phasemap_in_file'
-            elif input_vsm:
-                trait_spec.name_source = 'shift_in_file'
-            else:
-                raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
-                                   'fmap_in_file must be set.'))
-
-            trait_spec.output_name = 'shift_out_file'
+        if not isdefined(self.inputs.shift_out_file):
+            vsm_save_masked = (isdefined(self.inputs.save_shift) and self.inputs.save_shift)
+            vsm_save_unmasked = (isdefined(self.inputs.save_unmasked_shift) and
+                                 self.inputs.save_unmasked_shift)
+
+            if (vsm_save_masked or vsm_save_unmasked):
+                trait_spec = self.inputs.trait('shift_out_file')
+                trait_spec.output_name = 'shift_out_file'
+
+                if input_fmap:
+                    trait_spec.name_source = 'fmap_in_file'
+                elif input_phase:
+                    trait_spec.name_source = 'phasemap_in_file'
+                elif input_vsm:
+                    trait_spec.name_source = 'shift_in_file'
+                else:
+                    raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
+                                       'fmap_in_file must be set.'))
 
-            if vsm_save_unmasked:
-                trait_spec.name_template = '%s_vsm_unmasked'
+                if vsm_save_unmasked:
+                    trait_spec.name_template = '%s_vsm_unmasked'
+                else:
+                    trait_spec.name_template = '%s_vsm'
             else:
-                trait_spec.name_template = '%s_vsm'
+                skip += ['save_shift', 'save_unmasked_shift', 'shift_out_file']
 
         # Handle fieldmap output
-        fmap_save_masked = isdefined(self.inputs.save_fmap) and self.inputs.save_shift
-        fmap_save_unmasked = (isdefined(self.inputs.save_unmasked_fmap) and
-                              self.inputs.save_unmasked_fmap)
-
-        if ((fmap_save_masked or fmap_save_unmasked) and
-            not isdefined(self.inputs.fmap_out_file)):
-            trait_spec = self.inputs.trait('fmap_out_file')
-
-            if input_vsm:
-                trait_spec.name_source = 'shift_in_file'
-            elif input_phase:
-                trait_spec.name_source = 'phasemap_in_file'
-            elif input_fmap:
-                trait_spec.name_source = 'fmap_in_file'
-            else:
-                raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
-                                   'fmap_in_file must be set.'))
-
-            trait_spec.output_name = 'fmap_out_file'
+        if not isdefined(self.inputs.fmap_out_file):
+            fmap_save_masked = (isdefined(self.inputs.save_fmap) and self.inputs.save_fmap)
+            fmap_save_unmasked = (isdefined(self.inputs.save_unmasked_fmap) and
+                                 self.inputs.save_unmasked_fmap)
+
+            if (fmap_save_masked or fmap_save_unmasked):
+                trait_spec = self.inputs.trait('fmap_out_file')
+                trait_spec.output_name = 'fmap_out_file'
+
+                if input_vsm:
+                    trait_spec.name_source = 'shift_in_file'
+                elif input_phase:
+                    trait_spec.name_source = 'phasemap_in_file'
+                elif input_fmap:
+                    trait_spec.name_source = 'fmap_in_file'
+                else:
+                    raise RuntimeError(('Either phasemap_in_file, shift_in_file or '
+                                       'fmap_in_file must be set.'))
 
-            if fmap_save_unmasked:
-                trait_spec.name_template = '%s_fieldmap_unmasked'
+                if fmap_save_unmasked:
+                    trait_spec.name_template = '%s_fieldmap_unmasked'
+                else:
+                    trait_spec.name_template = '%s_fieldmap'
             else:
-                trait_spec.name_template = '%s_fieldmap'
+                skip += ['save_fmap', 'save_unmasked_fmap', 'fmap_out_file']
+
+        print skip
 
         return super(FUGUE, self)._parse_inputs(skip=skip)
 

From 4015325483ec96d28771797a397836a0f9fdaa62 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 8 Jul 2014 12:44:26 +0200
Subject: [PATCH 11/11] Remove spurious print

---
 nipype/interfaces/fsl/preprocess.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py
index 21ac7940e7..7e6e2f1756 100644
--- a/nipype/interfaces/fsl/preprocess.py
+++ b/nipype/interfaces/fsl/preprocess.py
@@ -1380,8 +1380,6 @@ def _parse_inputs(self, skip=None):
             else:
                 skip += ['save_fmap', 'save_unmasked_fmap', 'fmap_out_file']
 
-        print skip
-
         return super(FUGUE, self)._parse_inputs(skip=skip)