From 8a824cb9dac256abcad86da069eb1c312d533713 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 26 Jan 2017 16:27:54 -0800
Subject: [PATCH 01/48] partial implementation of an interface for
 antsMotionCorr. Outputs still need work, will only handle a single metric
 type and do basic transformation

---
 nipype/interfaces/ants/preprocess.py | 182 +++++++++++++++++++++++++++
 1 file changed, 182 insertions(+)
 create mode 100644 nipype/interfaces/ants/preprocess.py

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
new file mode 100644
index 0000000000..df1e1f7282
--- /dev/null
+++ b/nipype/interfaces/ants/preprocess.py
@@ -0,0 +1,182 @@
+# -*- coding: utf-8 -*-
+"""The ants module provides basic functions for interfacing with ants
+    functions.
+
+   Change directory to provide relative paths for doctests
+   >>> import os
+   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
+   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
+   >>> os.chdir(datadir)
+"""
+import os
+
+from ..base import TraitedSpec, File, traits, isdefined
+from .base import ANTSCommand, ANTSCommandInputSpec
+
+def _extant(field):
+    return (field is not None) and isdefined(field)
+
+class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
+    '''Input spec for the antsMotionCorr command.'''
+    dimension_desc = (
+        "This option forces the image to be treated as a "
+        "specified-dimensional image. If not specified, N4 tries to infer "
+        "the dimensionality from the input image."
+    )
+    dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=False,
+                                 position=0, desc=dimension_desc)
+
+    average_image = File(argstr='-a %s', position=1,
+                         desc="Average the input time series image.")
+
+    output_average_image = File(argstr="%s", hash_files=False, desc="")
+    output_transform_prefix = traits.Str()
+    output_warped_image = File(hash_files=False, desc="")
+
+    metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
+                              "Mattes", argstr="%s")
+    fixed_image = File(hash_files=False, desc="")
+    moving_image = File(hash_files=False, desc="")
+    metric_weight = traits.Float(1.0)
+    radius_or_bins = traits.Int(desc="")
+    sampling_strategy = traits.Enum("None", "Regular", "Random", None)
+    sampling_percentage = traits.Either(traits.Range(low=0.0, high=1.0), None)
+
+    transformation_model = traits.Enum("Affine", "Rigid", argstr="%s")
+    gradient_step_length = traits.Float(requires=['transformation_model'],
+                                        desc='')
+
+    iterations = traits.Int(
+        argstr="-i %d",
+        desc="Specify the number of iterations at each level."
+    )
+    smoothing_sigmas = traits.Int(
+        argstr="-s %d",
+        desc="Specify the amount of smoothing at each level."
+    )
+    shrink_factors = traits.Int(
+        argstr="-f %d",
+        desc=("Specify the shrink factor for the virtual domain (typically "
+              "the fixed image) at each level.")
+    )
+    n_images = traits.Int(
+        argstr="-n %d",
+        desc=("This option sets the number of images to use to construct the "
+              "template image.")
+    )
+    use_fixed_reference_image = traits.Bool(
+        argstr="-u %d",
+        default=True,
+        desc=("use a fixed reference image instead of the neighor in the time "
+              "series.")
+    )
+    use_scales_estimator = traits.Bool(
+        argstr="-e %d",
+        default=True,
+        desc="use the scale estimator to control optimization."
+    )
+
+class AntsMotionCorrOutputSpec(TraitedSpec):
+    '''Output spec for the antsMotionCorr command'''
+    average_image = File(exists=True, desc='Average of an image')
+    composite_transform = File(exists=True, desc='Composite transform file')
+    inverse_composite_transform = File(desc='Inverse composite transform file')
+    warped_image = File(desc="Outputs warped image")
+    inverse_warped_image = File(desc="Outputs the inverse of the warped image")
+    save_state = File(desc="The saved registration state to be restored")
+
+class AntsMotionCorr(ANTSCommand):
+    '''
+    Examples
+    -------
+    >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
+    >>> ants_mc = AntsMotionCorr()
+    >>> ants_mc.inputs.dimensionality = 3
+    >>> ants_mc.inputs.output_transform_prefix = "motcorr"
+    >>> ants_mc.inputs.output_warped_image = "warped.nii.gz"
+    >>> ants_mc.inputs.output_average_image = "average_image.nii.gz"
+    >>> ants_mc.inputs.metric_type = "GC"
+    >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
+    >>> ants_mc.inputs.moving_image = "input.nii.gz"
+    >>> ants_mc.inputs.metric_weight = 1
+    >>> ants_mc.inputs.radius_or_bins = 1
+    >>> ants_mc.inputs.sampling_strategy = "Random"
+    >>> ants_mc.inputs.sampling_percentage = 0.05
+    >>> ants_mc.inputs.transformation_model = "Affine"
+    >>> ants_mc.inputs.gradient_step_length = 0.005
+    >>> ants_mc.inputs.iterations = 10
+    >>> ants_mc.inputs.smoothing_sigmas = 0
+    >>> ants_mc.inputs.shrink_factors = 1
+    >>> ants_mc.inputs.n_images = 10
+    >>> ants_mc.inputs.use_fixed_reference_image = True
+    >>> ants_mc.inputs.use_scales_estimator = True
+    >>> print(ants_mc.cmdline)
+    antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
+    '''
+    _cmd = 'antsMotionCorr'
+    input_spec = AntsMotionCorrInputSpec
+    output_spec = AntsMotionCorrOutputSpec
+
+
+    def _gen_filename(self, name):
+        return None
+
+    def _format_arg(self, opt, spec, val):
+        if opt == 'metric_type':
+            return self._format_metric()
+        if opt == 'transformation_model':
+            return self._format_transform()
+        if opt == 'output_average_image':
+            return self._format_output()
+        return super(AntsMotionCorr, self)._format_arg(opt, spec, val)
+
+    def _format_metric(self):
+        metric_str = ("-m {metric_type}[{fixed_image},{moving_image},"
+                      "{metric_weight},{radius_or_bins},{sampling_strategy},"
+                      "{sampling_percentage}]")
+        format_args = {}
+        if _extant(self.inputs.metric_type):
+            format_args['metric_type'] = self.inputs.metric_type
+        if _extant(self.inputs.fixed_image):
+            format_args['fixed_image'] = self.inputs.fixed_image
+        if _extant(self.inputs.moving_image):
+            format_args['moving_image'] = self.inputs.moving_image
+        if _extant(self.inputs.metric_weight):
+            format_args['metric_weight'] = self.inputs.metric_weight
+        if _extant(self.inputs.sampling_strategy):
+            format_args['sampling_strategy'] = self.inputs.sampling_strategy
+        if _extant(self.inputs.sampling_percentage):
+            format_args['sampling_percentage'] = self.inputs.sampling_percentage
+        if _extant(self.inputs.radius_or_bins):
+            format_args['radius_or_bins'] = self.inputs.radius_or_bins
+        return metric_str.format(**format_args)
+
+    def _format_transform(self):
+        transform_str = "-t {}[{}]"
+        if (_extant(self.inputs.transformation_model)
+                and _extant(self.inputs.gradient_step_length)):
+            return transform_str.format(self.inputs.transformation_model,
+                                        self.inputs.gradient_step_length)
+        return ""
+
+    def _format_output(self):
+        if (_extant(self.inputs.output_transform_prefix)
+                and _extant(self.inputs.output_warped_image)
+                and _extant(self.inputs.output_average_image)):
+            return "-o [{},{},{}]".format(
+                self.inputs.output_transform_prefix,
+                self.inputs.output_warped_image,
+                self.inputs.output_average_image
+            )
+        elif _extant(self.inputs.output_average_image):
+            return "-o {}".format(self.inputs.output_average_image)
+        return ""
+
+    # motcorr_avg.nii.gz  motcorrMOCOparams.csv  motcorr.nii.gz
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        if _extant(self.inputs.output_average_image):
+            outputs['average_image'] = (
+                os.path.abspath(self.inputs.output_average_image)
+            )
+        return outputs

From 1e17d9e766319a9123dda0b3eecbe7c79956f1f4 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 27 Jan 2017 13:32:22 -0800
Subject: [PATCH 02/48] add documentation on where transformation format comes
 from. Added requires tags to metric arguments, and simplified processing of
 the metric argument formatting.

---
 nipype/interfaces/ants/preprocess.py | 39 ++++++++++++++--------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index df1e1f7282..3abe033a9f 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -35,12 +35,15 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")
-    fixed_image = File(hash_files=False, desc="")
-    moving_image = File(hash_files=False, desc="")
-    metric_weight = traits.Float(1.0)
-    radius_or_bins = traits.Int(desc="")
-    sampling_strategy = traits.Enum("None", "Regular", "Random", None)
-    sampling_percentage = traits.Either(traits.Range(low=0.0, high=1.0), None)
+    fixed_image = File(hash_files=False, requires=['metric_type'], desc="")
+    moving_image = File(hash_files=False, requires=['metric_type'],
+                        desc="This is the 4d image to be motion corrected")
+    metric_weight = traits.Float(1.0, requires=['metric_type'])
+    radius_or_bins = traits.Int(desc="", requires=['metric_type'])
+    sampling_strategy = traits.Enum("None", "Regular", "Random", None,
+                                    requires=['metric_type'])
+    sampling_percentage = traits.Either(traits.Range(low=0.0, high=1.0), None,
+                                        requires=['metric_type'])
 
     transformation_model = traits.Enum("Affine", "Rigid", argstr="%s")
     gradient_step_length = traits.Float(requires=['transformation_model'],
@@ -112,6 +115,10 @@ class AntsMotionCorr(ANTSCommand):
     >>> ants_mc.inputs.use_scales_estimator = True
     >>> print(ants_mc.cmdline)
     antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
+
+    Format and description of the affine motion correction parameters can in 
+    this PDF starting on page 555 section 3.9.16 AffineTransform:
+    https://itk.org/ItkSoftwareGuide.pdf
     '''
     _cmd = 'antsMotionCorr'
     input_spec = AntsMotionCorrInputSpec
@@ -135,20 +142,12 @@ def _format_metric(self):
                       "{metric_weight},{radius_or_bins},{sampling_strategy},"
                       "{sampling_percentage}]")
         format_args = {}
-        if _extant(self.inputs.metric_type):
-            format_args['metric_type'] = self.inputs.metric_type
-        if _extant(self.inputs.fixed_image):
-            format_args['fixed_image'] = self.inputs.fixed_image
-        if _extant(self.inputs.moving_image):
-            format_args['moving_image'] = self.inputs.moving_image
-        if _extant(self.inputs.metric_weight):
-            format_args['metric_weight'] = self.inputs.metric_weight
-        if _extant(self.inputs.sampling_strategy):
-            format_args['sampling_strategy'] = self.inputs.sampling_strategy
-        if _extant(self.inputs.sampling_percentage):
-            format_args['sampling_percentage'] = self.inputs.sampling_percentage
-        if _extant(self.inputs.radius_or_bins):
-            format_args['radius_or_bins'] = self.inputs.radius_or_bins
+        metric_args = ["metric_type", "fixed_image", "moving_image",
+                       "metric_weight", "radius_or_bins", "sampling_strategy",
+                       "sampling_percentage"]
+        for metric_arg in metric_args:
+            if _extant(getattr(self.inputs, metric_arg)):
+                format_args[metric_arg] = getattr(self.inputs, metric_arg)
         return metric_str.format(**format_args)
 
     def _format_transform(self):

From 3b0ccfa4b0aa828ab3b9cb68bee099d57715a4b4 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 27 Jan 2017 15:31:28 -0800
Subject: [PATCH 03/48] first attempt at adding antsMotionCorrStats interface.
 Added more outputs to antsMotionCorr in list outputs

---
 nipype/interfaces/ants/preprocess.py | 49 ++++++++++++++++++++++++++--
 1 file changed, 47 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 3abe033a9f..5617d8d82d 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -13,9 +13,46 @@
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import ANTSCommand, ANTSCommandInputSpec
 
+
 def _extant(field):
     return (field is not None) and isdefined(field)
 
+class AntsMotionCorrStatsInputSpec(ANTSCommandInputSpec):
+    ''' Input spec for the antsMotionCorrStats command '''
+    mask = File(argstr="-x %s", mandatory=True,
+                desc="compute displacements within specified mask.")
+    moco = File(
+        argstr="-m %s", mandatory=True,
+        desc="motion correction parameter file to calculate statistics on"
+    )
+    output = File(argstr="-o %s", hash_files=False, mandatory=True,
+                  desc="csv file to output calculated statistics into")
+    framewise = traits.Bool(argstr="-f %d",
+                            desc="do framwise summarywise stats")
+    output_spatial_map = File(argstr='-s %s', hash_files=False,
+                              desc="File to output displacement magnitude to.")
+
+class AntsMotionCorrStatsOutputSpec(TraitedSpec):
+    ''' Output spec for the antsMotionCorrStats command '''
+    spatial_map = File(exists=True)
+    output = File(exists=True)
+
+class AntsMotionCorrStats(ANTSCommand):
+    ''' Interface for the antsMotionCorrStats command '''
+
+    def _gen_filename(self, name):
+        return None
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        if _extant(self.inputs.output_spatial_map):
+            outputs['spatial_map'] = (
+                os.path.abspath(self.inputs.output_spatial_map)
+            )
+        if _extant(self.inputs.output):
+            outputs['output'] = os.path.abspath(self.inputs.output)
+        return outputs
+
 class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     '''Input spec for the antsMotionCorr command.'''
     dimension_desc = (
@@ -116,8 +153,8 @@ class AntsMotionCorr(ANTSCommand):
     >>> print(ants_mc.cmdline)
     antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
 
-    Format and description of the affine motion correction parameters can in 
-    this PDF starting on page 555 section 3.9.16 AffineTransform:
+    Format and description of the affine motion correction parameters can be
+    found in this PDF starting on page 555 section 3.9.16 AffineTransform:
     https://itk.org/ItkSoftwareGuide.pdf
     '''
     _cmd = 'antsMotionCorr'
@@ -178,4 +215,12 @@ def _list_outputs(self):
             outputs['average_image'] = (
                 os.path.abspath(self.inputs.output_average_image)
             )
+        if _extant(self.inputs.output_warped_image):
+            outputs['warped_image'] = (
+                os.path.abspath(self.inputs.output_warped_image)
+            )
+        if _extant(self.inputs.output_transform_prefix):
+            outputs['composite_transform'] = '{}MOCOparams.csv'.format(
+                self.inputs.output_tranform_prefix
+            )
         return outputs

From 47df18129e7f42740cca8f90b1813d597d6ff177 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 27 Jan 2017 16:46:04 -0800
Subject: [PATCH 04/48] add a gen_filename entry for output_average_image in
 antsMotionCorr, added default to dimensionality

---
 nipype/interfaces/ants/preprocess.py | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 5617d8d82d..ad0d164804 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -12,6 +12,7 @@
 
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import ANTSCommand, ANTSCommandInputSpec
+from ..utils.filemanip import split_filename
 
 
 def _extant(field):
@@ -61,19 +62,19 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
         "the dimensionality from the input image."
     )
     dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=False,
-                                 position=0, desc=dimension_desc)
+                                 position=0, desc=dimension_desc, default=3)
 
     average_image = File(argstr='-a %s', position=1,
                          desc="Average the input time series image.")
 
-    output_average_image = File(argstr="%s", hash_files=False, desc="")
+    output_average_image = File(argstr="%s", hash_files=False, desc="", genfile)
     output_transform_prefix = traits.Str()
     output_warped_image = File(hash_files=False, desc="")
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")
-    fixed_image = File(hash_files=False, requires=['metric_type'], desc="")
-    moving_image = File(hash_files=False, requires=['metric_type'],
+    fixed_image = File(requires=['metric_type'], desc="")
+    moving_image = File(requires=['metric_type'],
                         desc="This is the 4d image to be motion corrected")
     metric_weight = traits.Float(1.0, requires=['metric_type'])
     radius_or_bins = traits.Int(desc="", requires=['metric_type'])
@@ -163,6 +164,10 @@ class AntsMotionCorr(ANTSCommand):
 
 
     def _gen_filename(self, name):
+        if name == 'output_average_image' and _extant(self.inputs.average):
+            pth, fname, ext = split_filename(self.inputs.average)
+            new_fname = '{}{}{}'.format(fname, '_avg', ext)
+            return os.path.join(pth, new_fname)
         return None
 
     def _format_arg(self, opt, spec, val):

From 39d986a41f43e056d895a14dedf0769631b4759a Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 30 Jan 2017 10:42:02 -0800
Subject: [PATCH 05/48] fix syntax errors in ants preprocess

---
 nipype/interfaces/ants/preprocess.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index ad0d164804..8a47911bf1 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -12,7 +12,7 @@
 
 from ..base import TraitedSpec, File, traits, isdefined
 from .base import ANTSCommand, ANTSCommandInputSpec
-from ..utils.filemanip import split_filename
+from ...utils.filemanip import split_filename
 
 
 def _extant(field):
@@ -67,7 +67,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     average_image = File(argstr='-a %s', position=1,
                          desc="Average the input time series image.")
 
-    output_average_image = File(argstr="%s", hash_files=False, desc="", genfile)
+    output_average_image = File(argstr="%s", hash_files=False, desc="", genfile=True)
     output_transform_prefix = traits.Str()
     output_warped_image = File(hash_files=False, desc="")
 

From 3b5f99d1feb17e45fe6790f892ae5bc4eddd426b Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Feb 2017 16:11:48 -0800
Subject: [PATCH 06/48] get argstrs in line for ants motion correction

---
 nipype/interfaces/ants/preprocess.py | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 8a47911bf1..56283bd8df 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -61,15 +61,17 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
         "specified-dimensional image. If not specified, N4 tries to infer "
         "the dimensionality from the input image."
     )
-    dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=False,
+    dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=True,
                                  position=0, desc=dimension_desc, default=3)
 
-    average_image = File(argstr='-a %s', position=1,
+    average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
 
-    output_average_image = File(argstr="%s", hash_files=False, desc="", genfile=True)
+    output_average_image = File(hash_files=False, desc="", argstr="%s",
+                                genfile=True, exists=False, usedefault=True)
     output_transform_prefix = traits.Str()
-    output_warped_image = File(hash_files=False, desc="")
+    output_warped_image = File(hash_files=False, desc="",
+                               exists=False)
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")
@@ -120,7 +122,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
 class AntsMotionCorrOutputSpec(TraitedSpec):
     '''Output spec for the antsMotionCorr command'''
     average_image = File(exists=True, desc='Average of an image')
-    composite_transform = File(exists=True, desc='Composite transform file')
+    composite_transform = File(desc='Composite transform file')
     inverse_composite_transform = File(desc='Inverse composite transform file')
     warped_image = File(desc="Outputs warped image")
     inverse_warped_image = File(desc="Outputs the inverse of the warped image")
@@ -164,10 +166,17 @@ class AntsMotionCorr(ANTSCommand):
 
 
     def _gen_filename(self, name):
-        if name == 'output_average_image' and _extant(self.inputs.average):
-            pth, fname, ext = split_filename(self.inputs.average)
+        if name == 'output_average_image':
+            if _extant(self.inputs.average_image):
+                pth, fname, ext = split_filename(self.inputs.average_image)
+            else:
+                pth, fname, ext = split_filename(self.inputs.fixed_image)
             new_fname = '{}{}{}'.format(fname, '_avg', ext)
             return os.path.join(pth, new_fname)
+        if name == 'ouput_warped_image' and _extant(self.inputs.fixed_image):
+            pth, fname, ext = split_filename(self.inputs.fixed_image)
+            new_fname = '{}{}{}'.format(fname, '_warped', ext)
+            return os.path.join(pth, new_fname)
         return None
 
     def _format_arg(self, opt, spec, val):
@@ -176,6 +185,7 @@ def _format_arg(self, opt, spec, val):
         if opt == 'transformation_model':
             return self._format_transform()
         if opt == 'output_average_image':
+            self.inputs.output_average_image = self._gen_filename("output_average_image")
             return self._format_output()
         return super(AntsMotionCorr, self)._format_arg(opt, spec, val)
 
@@ -198,7 +208,7 @@ def _format_transform(self):
                 and _extant(self.inputs.gradient_step_length)):
             return transform_str.format(self.inputs.transformation_model,
                                         self.inputs.gradient_step_length)
-        return ""
+        return " bad format "
 
     def _format_output(self):
         if (_extant(self.inputs.output_transform_prefix)
@@ -226,6 +236,6 @@ def _list_outputs(self):
             )
         if _extant(self.inputs.output_transform_prefix):
             outputs['composite_transform'] = '{}MOCOparams.csv'.format(
-                self.inputs.output_tranform_prefix
+                self.inputs.output_transform_prefix
             )
         return outputs

From 1c57878ba2709c318b52951ac531ffbe8c6b0de0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 13 Feb 2017 21:57:41 -0800
Subject: [PATCH 07/48] add interface to convert ants motion correction
 matrices to fsl style motion parameters

---
 nipype/interfaces/ants/preprocess.py          | 72 +++++++++++++++-
 .../ants/tests/test_auto_AntsMotionCorr.py    | 83 +++++++++++++++++++
 .../tests/test_auto_AntsMotionCorrStats.py    | 25 ++++++
 .../tests/test_auto_antsBrainExtraction.py    | 16 ++++
 4 files changed, 192 insertions(+), 4 deletions(-)
 create mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
 create mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 56283bd8df..1057385d6c 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -8,9 +8,14 @@
    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
    >>> os.chdir(datadir)
 """
+import csv
+import math
 import os
-
-from ..base import TraitedSpec, File, traits, isdefined
+ 
+from nipype.interfaces.base import BaseInterface, \
+    BaseInterfaceInputSpec, traits, File, TraitedSpec
+from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
+                    traits, isdefined)
 from .base import ANTSCommand, ANTSCommandInputSpec
 from ...utils.filemanip import split_filename
 
@@ -26,7 +31,7 @@ class AntsMotionCorrStatsInputSpec(ANTSCommandInputSpec):
         argstr="-m %s", mandatory=True,
         desc="motion correction parameter file to calculate statistics on"
     )
-    output = File(argstr="-o %s", hash_files=False, mandatory=True,
+    output = File(argstr="-o %s", hash_files=False, genfile=True,
                   desc="csv file to output calculated statistics into")
     framewise = traits.Bool(argstr="-f %d",
                             desc="do framwise summarywise stats")
@@ -41,7 +46,13 @@ class AntsMotionCorrStatsOutputSpec(TraitedSpec):
 class AntsMotionCorrStats(ANTSCommand):
     ''' Interface for the antsMotionCorrStats command '''
 
+    _cmd = 'antsMotionCorrStats'
+    input_spec = AntsMotionCorrStatsInputSpec
+    output_spec = AntsMotionCorrStatsOutputSpec
+
     def _gen_filename(self, name):
+        if name == 'output':
+            return "frame_displacement.csv"
         return None
 
     def _list_outputs(self):
@@ -107,18 +118,21 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
         desc=("This option sets the number of images to use to construct the "
               "template image.")
     )
+
     use_fixed_reference_image = traits.Bool(
         argstr="-u %d",
         default=True,
         desc=("use a fixed reference image instead of the neighor in the time "
               "series.")
     )
+
     use_scales_estimator = traits.Bool(
         argstr="-e %d",
         default=True,
         desc="use the scale estimator to control optimization."
     )
 
+
 class AntsMotionCorrOutputSpec(TraitedSpec):
     '''Output spec for the antsMotionCorr command'''
     average_image = File(exists=True, desc='Average of an image')
@@ -235,7 +249,57 @@ def _list_outputs(self):
                 os.path.abspath(self.inputs.output_warped_image)
             )
         if _extant(self.inputs.output_transform_prefix):
-            outputs['composite_transform'] = '{}MOCOparams.csv'.format(
+            fname = '{}MOCOparams.csv'.format(
                 self.inputs.output_transform_prefix
             )
+            outputs['composite_transform'] = os.path.abspath(fname)
+        return outputs
+
+class AntsMatrixConversionInputSpec(BaseInterfaceInputSpec):
+    matrix = File(
+        exists=True,
+        desc='Motion crrection matrices to be converted into FSL style motion parameters',
+        mandatory=True
+    )
+
+class AntsMatrixConversionOutputSpec(TraitedSpec):
+    parameters = File(exists=True, desc="parameters to be output")
+
+
+class AntsMatrixConversion(BaseInterface):
+    ''' Take antsMotionCorr motion output as input, convert to FSL style parameter files'''
+    input_spec = AntsMatrixConversionInputSpec
+    output_spec = AntsMatrixConversionOutputSpec
+
+    def _run_interface(self, runtime):
+        in_fp = open(self.inputs.matrix)
+        in_data = csv.reader(in_fp)
+        pars = []
+
+        # Ants motion correction output has a single line header that we ignore
+        next(in_data)
+
+        for x in in_data:
+            t1 = math.atan2(float(x[7]), float(x[10]))
+            c2 = math.sqrt((float(x[2]) * float(x[2])) + (float(x[3]) * float(x[3])))
+            t2 = math.atan2(-float(x[4]), c2)
+            t3 = math.atan2(float(x[3]), float(x[2]))
+            parameters = "{:.8f} {:.8f} {:.8f} {:.8f} {:.8f} {:.8f}"
+            pars.append(parameters.format(t1, t2, t3, float(x[11]), float(x[12]),
+                                          float(x[13])))
+
+        pth, fname, _ = split_filename(self.inputs.matrix)
+        new_fname = '{}{}'.format(fname, '.par')
+        parameters = os.path.join(pth, new_fname)
+        with open(parameters, mode='wt') as out_fp:
+            out_fp.write('\n'.join(pars))
+        in_fp.close()
+        return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        pth, fname, _ = split_filename(self.inputs.matrix)
+        new_fname = '{}{}'.format(fname, '.par')
+        out_file = os.path.join(pth, new_fname)
+        outputs["parameters"] = out_file
         return outputs
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
new file mode 100644
index 0000000000..426fc9f959
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
@@ -0,0 +1,83 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..preprocess import AntsMotionCorr
+
+
+def test_AntsMotionCorr_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    average_image=dict(argstr='-a %s',
+    position=1,
+    ),
+    dimensionality=dict(argstr='-d %d',
+    position=0,
+    usedefault=False,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fixed_image=dict(requires=['metric_type'],
+    ),
+    gradient_step_length=dict(requires=['transformation_model'],
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    iterations=dict(argstr='-i %d',
+    ),
+    metric_type=dict(argstr='%s',
+    ),
+    metric_weight=dict(requires=['metric_type'],
+    ),
+    moving_image=dict(requires=['metric_type'],
+    ),
+    n_images=dict(argstr='-n %d',
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    output_average_image=dict(argstr='%s',
+    genfile=True,
+    hash_files=False,
+    ),
+    output_transform_prefix=dict(),
+    output_warped_image=dict(hash_files=False,
+    ),
+    radius_or_bins=dict(requires=['metric_type'],
+    ),
+    sampling_percentage=dict(requires=['metric_type'],
+    ),
+    sampling_strategy=dict(requires=['metric_type'],
+    ),
+    shrink_factors=dict(argstr='-f %d',
+    ),
+    smoothing_sigmas=dict(argstr='-s %d',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    transformation_model=dict(argstr='%s',
+    ),
+    use_fixed_reference_image=dict(argstr='-u %d',
+    ),
+    use_scales_estimator=dict(argstr='-e %d',
+    ),
+    )
+    inputs = AntsMotionCorr.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_AntsMotionCorr_outputs():
+    output_map = dict(average_image=dict(),
+    composite_transform=dict(),
+    inverse_composite_transform=dict(),
+    inverse_warped_image=dict(),
+    save_state=dict(),
+    warped_image=dict(),
+    )
+    outputs = AntsMotionCorr.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
new file mode 100644
index 0000000000..09fb98b3d7
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
@@ -0,0 +1,25 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..preprocess import AntsMotionCorrStats
+
+
+def test_AntsMotionCorrStats_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = AntsMotionCorrStats.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
diff --git a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py
index 9abcaa99bb..7597105a3f 100644
--- a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py
+++ b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py
@@ -55,7 +55,23 @@ def test_antsBrainExtraction_inputs():
 
 def test_antsBrainExtraction_outputs():
     output_map = dict(BrainExtractionBrain=dict(),
+    BrainExtractionCSF=dict(),
+    BrainExtractionGM=dict(),
+    BrainExtractionInitialAffine=dict(),
+    BrainExtractionInitialAffineFixed=dict(),
+    BrainExtractionInitialAffineMoving=dict(),
+    BrainExtractionLaplacian=dict(),
     BrainExtractionMask=dict(),
+    BrainExtractionPrior0GenericAffine=dict(),
+    BrainExtractionPrior1InverseWarp=dict(),
+    BrainExtractionPrior1Warp=dict(),
+    BrainExtractionPriorWarped=dict(),
+    BrainExtractionSegmentation=dict(),
+    BrainExtractionTemplateLaplacian=dict(),
+    BrainExtractionTmp=dict(),
+    BrainExtractionWM=dict(),
+    N4Corrected0=dict(),
+    N4Truncated0=dict(),
     )
     outputs = antsBrainExtraction.output_spec()
 

From 06de3051c39a9acc0b872afdc7b38767e0f264e2 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 11:25:54 -0800
Subject: [PATCH 08/48] fixup input spec

---
 nipype/interfaces/ants/preprocess.py | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 1057385d6c..8af6f0825f 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -12,8 +12,8 @@
 import math
 import os
  
-from nipype.interfaces.base import BaseInterface, \
-    BaseInterfaceInputSpec, traits, File, TraitedSpec
+from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec,
+                                    traits, File, TraitedSpec)
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
                     traits, isdefined)
 from .base import ANTSCommand, ANTSCommandInputSpec
@@ -78,15 +78,14 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
 
-    output_average_image = File(hash_files=False, desc="", argstr="%s",
-                                genfile=True, exists=False, usedefault=True)
+    output_average_image = traits.Str(desc="Filename to save average of input image as.", argstr="%s")
+                                
     output_transform_prefix = traits.Str()
-    output_warped_image = File(hash_files=False, desc="",
-                               exists=False)
+    output_warped_image = Str(desc="Name to save motion corrected image as.")
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")
-    fixed_image = File(requires=['metric_type'], desc="")
+    fixed_image = File(requires=['metric_type'], desc="Fixed image to do motion correction with respect to.")
     moving_image = File(requires=['metric_type'],
                         desc="This is the 4d image to be motion corrected")
     metric_weight = traits.Float(1.0, requires=['metric_type'])
@@ -120,15 +119,15 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     )
 
     use_fixed_reference_image = traits.Bool(
+        True,
         argstr="-u %d",
-        default=True,
         desc=("use a fixed reference image instead of the neighor in the time "
               "series.")
     )
 
     use_scales_estimator = traits.Bool(
+        True,
         argstr="-e %d",
-        default=True,
         desc="use the scale estimator to control optimization."
     )
 
@@ -237,7 +236,6 @@ def _format_output(self):
             return "-o {}".format(self.inputs.output_average_image)
         return ""
 
-    # motcorr_avg.nii.gz  motcorrMOCOparams.csv  motcorr.nii.gz
     def _list_outputs(self):
         outputs = self._outputs().get()
         if _extant(self.inputs.output_average_image):

From df7204090fa159348b6bb43e320f0428b1f8c1f8 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 11:29:28 -0800
Subject: [PATCH 09/48] add descriptions to antsmotioncorrstats outputs

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

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 8af6f0825f..3781ef2a2f 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -40,8 +40,8 @@ class AntsMotionCorrStatsInputSpec(ANTSCommandInputSpec):
 
 class AntsMotionCorrStatsOutputSpec(TraitedSpec):
     ''' Output spec for the antsMotionCorrStats command '''
-    spatial_map = File(exists=True)
-    output = File(exists=True)
+    spatial_map = File(desc="output image of displacement magnitude", exists=True)
+    output = File(desc="CSV file containg motion correction statistics", exists=True)
 
 class AntsMotionCorrStats(ANTSCommand):
     ''' Interface for the antsMotionCorrStats command '''
@@ -73,7 +73,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
         "the dimensionality from the input image."
     )
     dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=True,
-                                 position=0, desc=dimension_desc, default=3)
+                                 position=0, desc=dimension_desc)
 
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
@@ -134,9 +134,9 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
 
 class AntsMotionCorrOutputSpec(TraitedSpec):
     '''Output spec for the antsMotionCorr command'''
-    average_image = File(exists=True, desc='Average of an image')
-    composite_transform = File(desc='Composite transform file')
-    inverse_composite_transform = File(desc='Inverse composite transform file')
+    average_image = File(exists=True, desc="Average of an image")
+    composite_transform = File(desc="Composite transform file")
+    inverse_composite_transform = File(desc="Inverse composite transform file")
     warped_image = File(desc="Outputs warped image")
     inverse_warped_image = File(desc="Outputs the inverse of the warped image")
     save_state = File(desc="The saved registration state to be restored")

From 99c9fb5c6fa3aee11dd66798ff38adad4db3a6f4 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 11:36:03 -0800
Subject: [PATCH 10/48] instantiate Str trait properly

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

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 3781ef2a2f..13b16c9571 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -81,7 +81,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     output_average_image = traits.Str(desc="Filename to save average of input image as.", argstr="%s")
                                 
     output_transform_prefix = traits.Str()
-    output_warped_image = Str(desc="Name to save motion corrected image as.")
+    output_warped_image = traits.Str(desc="Name to save motion corrected image as.")
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")

From 9bb5208f29b33b68e39a79c9cdf32ce46a13f182 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 11:39:32 -0800
Subject: [PATCH 11/48] remove trailing whitespace

---
 nipype/interfaces/ants/preprocess.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 13b16c9571..488f515eef 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -11,7 +11,7 @@
 import csv
 import math
 import os
- 
+
 from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec,
                                     traits, File, TraitedSpec)
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
@@ -79,7 +79,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
                          desc="Average the input time series image.")
 
     output_average_image = traits.Str(desc="Filename to save average of input image as.", argstr="%s")
-                                
+
     output_transform_prefix = traits.Str()
     output_warped_image = traits.Str(desc="Name to save motion corrected image as.")
 

From 691a7b59923253d3bac9724843ee4587706feb10 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 1 Mar 2017 14:46:03 -0800
Subject: [PATCH 12/48] Update preprocess.py

---
 nipype/interfaces/ants/preprocess.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 488f515eef..71ac8535eb 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -12,10 +12,8 @@
 import math
 import os
 
-from nipype.interfaces.base import (BaseInterface, BaseInterfaceInputSpec,
-                                    traits, File, TraitedSpec)
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
-                    traits, isdefined)
+                    traits, isdefined, Str)
 from .base import ANTSCommand, ANTSCommandInputSpec
 from ...utils.filemanip import split_filename
 
@@ -78,10 +76,10 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
 
-    output_average_image = traits.Str(desc="Filename to save average of input image as.", argstr="%s")
+    output_average_image = Str(desc="Filename to save average of input image as.", argstr="%s")
 
-    output_transform_prefix = traits.Str()
-    output_warped_image = traits.Str(desc="Name to save motion corrected image as.")
+    output_transform_prefix = Str()
+    output_warped_image = Str(desc="Name to save motion corrected image as.")
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
                               "Mattes", argstr="%s")

From 84c397de0308c640fdaea13eb137264e68d5066e Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 14:48:59 -0800
Subject: [PATCH 13/48] reorder genfilename logic

---
 nipype/interfaces/ants/preprocess.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 488f515eef..0c8e939c89 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -78,7 +78,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
 
-    output_average_image = traits.Str(desc="Filename to save average of input image as.", argstr="%s")
+    output_average_image = traits.File(desc="Filename to save average of input image as.", genfile=True)
 
     output_transform_prefix = traits.Str()
     output_warped_image = traits.Str(desc="Name to save motion corrected image as.")
@@ -180,10 +180,11 @@ class AntsMotionCorr(ANTSCommand):
 
     def _gen_filename(self, name):
         if name == 'output_average_image':
-            if _extant(self.inputs.average_image):
-                pth, fname, ext = split_filename(self.inputs.average_image)
-            else:
-                pth, fname, ext = split_filename(self.inputs.fixed_image)
+            if _extant(self.inputs.fixed_image):
+                return self.inputs.fixed_image
+            if not _extant(self.inputs.average_image):
+                raise ValueError("Either fixed_image or average_image must be defined")
+            pth, fname, ext = split_filename(self.inputs.average_image)
             new_fname = '{}{}{}'.format(fname, '_avg', ext)
             return os.path.join(pth, new_fname)
         if name == 'ouput_warped_image' and _extant(self.inputs.fixed_image):
@@ -198,8 +199,12 @@ def _format_arg(self, opt, spec, val):
         if opt == 'transformation_model':
             return self._format_transform()
         if opt == 'output_average_image':
-            self.inputs.output_average_image = self._gen_filename("output_average_image")
+            if not _extant(self.inputs.output_average_image):
+                self.inputs.output_average_image = self._gen_filename("output_average_image")
+            else:
+                self.inputs.output_average_image = "wat.nii.gz"
             return self._format_output()
+        self.inputs.output_average_image = "wat.nii.gz"
         return super(AntsMotionCorr, self)._format_arg(opt, spec, val)
 
     def _format_metric(self):

From 97b32efb77dca600e2fddee0736640a9aec93a89 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 15:18:20 -0800
Subject: [PATCH 14/48] fix output_average_image decleration.

---
 nipype/interfaces/ants/preprocess.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index d6acb8bc5b..4166fdde8a 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -76,9 +76,12 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="Average the input time series image.")
 
-    output_average_image = traits.File(desc="Filename to save average of input image as.", genfile=True)
+    output_average_image = traits.File(desc="Filename to save average of input image as.",
+                                       genfile=True, hash_files=False, argstr='%s')
 
-    output_transform_prefix = Str()
+    output_transform_prefix = Str(
+        desc="string to prepend to file containg all of the transformation parameters"
+    )
     output_warped_image = Str(desc="Name to save motion corrected image as.")
 
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
@@ -148,7 +151,6 @@ class AntsMotionCorr(ANTSCommand):
     >>> ants_mc.inputs.dimensionality = 3
     >>> ants_mc.inputs.output_transform_prefix = "motcorr"
     >>> ants_mc.inputs.output_warped_image = "warped.nii.gz"
-    >>> ants_mc.inputs.output_average_image = "average_image.nii.gz"
     >>> ants_mc.inputs.metric_type = "GC"
     >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
     >>> ants_mc.inputs.moving_image = "input.nii.gz"
@@ -197,10 +199,7 @@ def _format_arg(self, opt, spec, val):
         if opt == 'transformation_model':
             return self._format_transform()
         if opt == 'output_average_image':
-            if not _extant(self.inputs.output_average_image):
-                self.inputs.output_average_image = self._gen_filename("output_average_image")
-            else:
-                self.inputs.output_average_image = "wat.nii.gz"
+            self.inputs.output_average_image = self._gen_filename("output_average_image")
             return self._format_output()
         self.inputs.output_average_image = "wat.nii.gz"
         return super(AntsMotionCorr, self)._format_arg(opt, spec, val)

From ff516679c954f042a75fdad5e22f56af83136885 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 15:23:11 -0800
Subject: [PATCH 15/48] remove test wat

---
 nipype/interfaces/ants/preprocess.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 4166fdde8a..3e69960baa 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -201,7 +201,6 @@ def _format_arg(self, opt, spec, val):
         if opt == 'output_average_image':
             self.inputs.output_average_image = self._gen_filename("output_average_image")
             return self._format_output()
-        self.inputs.output_average_image = "wat.nii.gz"
         return super(AntsMotionCorr, self)._format_arg(opt, spec, val)
 
     def _format_metric(self):

From 722a51c919bea62e178b716a757ac17ccf50a915 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 1 Mar 2017 16:33:36 -0800
Subject: [PATCH 16/48] update example

---
 nipype/interfaces/ants/preprocess.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 3e69960baa..ab755814f3 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -147,25 +147,25 @@ class AntsMotionCorr(ANTSCommand):
     Examples
     -------
     >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
-    >>> ants_mc = AntsMotionCorr()
-    >>> ants_mc.inputs.dimensionality = 3
-    >>> ants_mc.inputs.output_transform_prefix = "motcorr"
-    >>> ants_mc.inputs.output_warped_image = "warped.nii.gz"
-    >>> ants_mc.inputs.metric_type = "GC"
-    >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
-    >>> ants_mc.inputs.moving_image = "input.nii.gz"
+    >>> ants_mc = AntsMotionCorr() 
+    >>> ants_mc.inputs.metric_type = 'GC'
     >>> ants_mc.inputs.metric_weight = 1
     >>> ants_mc.inputs.radius_or_bins = 1
     >>> ants_mc.inputs.sampling_strategy = "Random"
     >>> ants_mc.inputs.sampling_percentage = 0.05
-    >>> ants_mc.inputs.transformation_model = "Affine"
-    >>> ants_mc.inputs.gradient_step_length = 0.005
     >>> ants_mc.inputs.iterations = 10
     >>> ants_mc.inputs.smoothing_sigmas = 0
     >>> ants_mc.inputs.shrink_factors = 1
     >>> ants_mc.inputs.n_images = 10
     >>> ants_mc.inputs.use_fixed_reference_image = True
     >>> ants_mc.inputs.use_scales_estimator = True
+    >>> ants_mc.inputs.output_average_image = 'wat'
+    >>> ants_mc.inputs.output_warped_image = 'warped.nii.gz'
+    >>> ants_mc.inputs.output_transform_prefix = 'motcorr'
+    >>> ants_mc.inputs.transformation_model = 'Affine'
+    >>> ants_mc.inputs.gradient_step_length = 0.005
+    >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
+    >>> ants_mc.inputs.moving_image = "input.nii.gz"
     >>> print(ants_mc.cmdline)
     antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
 

From f4ab57e2e8350becb4965c516160dbef64cd59db Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 09:32:51 -0800
Subject: [PATCH 17/48] remake specs

---
 .../tests/test_auto_AntsMatrixConversion.py   | 27 +++++++++++++++++++
 .../ants/tests/test_auto_AntsMotionCorr.py    |  6 ++---
 .../tests/test_auto_AntsMotionCorrStats.py    | 26 ++++++++++++++++++
 3 files changed, 56 insertions(+), 3 deletions(-)
 create mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py

diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py b/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py
new file mode 100644
index 0000000000..f7ecb64d2b
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py
@@ -0,0 +1,27 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import AntsMatrixConversion
+
+
+def test_AntsMatrixConversion_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    matrix=dict(mandatory=True,
+    ),
+    )
+    inputs = AntsMatrixConversion.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_AntsMatrixConversion_outputs():
+    output_map = dict(parameters=dict(),
+    )
+    outputs = AntsMatrixConversion.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
index 426fc9f959..d340a437bf 100644
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..preprocess import AntsMotionCorr
 
 
@@ -10,7 +11,7 @@ def test_AntsMotionCorr_inputs():
     ),
     dimensionality=dict(argstr='-d %d',
     position=0,
-    usedefault=False,
+    usedefault=True,
     ),
     environ=dict(nohash=True,
     usedefault=True,
@@ -40,8 +41,7 @@ def test_AntsMotionCorr_inputs():
     hash_files=False,
     ),
     output_transform_prefix=dict(),
-    output_warped_image=dict(hash_files=False,
-    ),
+    output_warped_image=dict(),
     radius_or_bins=dict(requires=['metric_type'],
     ),
     sampling_percentage=dict(requires=['metric_type'],
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
index 09fb98b3d7..e81fb4f95d 100644
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
@@ -1,4 +1,5 @@
 # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
 from ..preprocess import AntsMotionCorrStats
 
 
@@ -8,12 +9,27 @@ def test_AntsMotionCorrStats_inputs():
     environ=dict(nohash=True,
     usedefault=True,
     ),
+    framewise=dict(argstr='-f %d',
+    ),
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
+    mask=dict(argstr='-x %s',
+    mandatory=True,
+    ),
+    moco=dict(argstr='-m %s',
+    mandatory=True,
+    ),
     num_threads=dict(nohash=True,
     usedefault=True,
     ),
+    output=dict(argstr='-o %s',
+    genfile=True,
+    hash_files=False,
+    ),
+    output_spatial_map=dict(argstr='-s %s',
+    hash_files=False,
+    ),
     terminal_output=dict(nohash=True,
     ),
     )
@@ -23,3 +39,13 @@ def test_AntsMotionCorrStats_inputs():
         for metakey, value in list(metadata.items()):
             assert getattr(inputs.traits()[key], metakey) == value
 
+
+def test_AntsMotionCorrStats_outputs():
+    output_map = dict(output=dict(),
+    spatial_map=dict(),
+    )
+    outputs = AntsMotionCorrStats.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

From f28151b7f161a9e7022a608c0eeb540028a9b2ad Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 10:59:54 -0800
Subject: [PATCH 18/48] add more descriptions

---
 nipype/interfaces/ants/preprocess.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index ab755814f3..d09db7f1b9 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -74,19 +74,28 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
                                  position=0, desc=dimension_desc)
 
     average_image = File(argstr='-a %s', position=1, exists=False,
-                         desc="Average the input time series image.")
+                         desc="4D image to take an average of.")
 
     output_average_image = traits.File(desc="Filename to save average of input image as.",
                                        genfile=True, hash_files=False, argstr='%s')
 
     output_transform_prefix = Str(
-        desc="string to prepend to file containg all of the transformation parameters"
+        desc="string to prepend to file containg the transformation parameters"
     )
     output_warped_image = Str(desc="Name to save motion corrected image as.")
 
+    metric_type_desc = (
+        "GC : global correlation, CC: ANTS neighborhood cross correlation, "
+        "MI: Mutual information, and Demons: Thirion's Demons "
+        "(modified mean-squares). Note that the metricWeight is currently not "
+        "used. Rather, it is a temporary place holder until multivariate "
+        "metrics are available for a single stage."
+    )
+
     metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
-                              "Mattes", argstr="%s")
-    fixed_image = File(requires=['metric_type'], desc="Fixed image to do motion correction with respect to.")
+                              "Mattes", argstr="%s", desc=metric_type_desc)
+    fixed_image = File(requires=['metric_type'],
+                       desc="Fixed image to do motion correction with respect to.")
     moving_image = File(requires=['metric_type'],
                         desc="This is the 4d image to be motion corrected")
     metric_weight = traits.Float(1.0, requires=['metric_type'])
@@ -147,7 +156,7 @@ class AntsMotionCorr(ANTSCommand):
     Examples
     -------
     >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
-    >>> ants_mc = AntsMotionCorr() 
+    >>> ants_mc = AntsMotionCorr()
     >>> ants_mc.inputs.metric_type = 'GC'
     >>> ants_mc.inputs.metric_weight = 1
     >>> ants_mc.inputs.radius_or_bins = 1

From 40edcbf2f467030d0cc2c7fff1ff82c9f7729c5a Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 12:14:34 -0800
Subject: [PATCH 19/48] fix output_average_image not taking user defined file
 name

---
 nipype/interfaces/ants/preprocess.py | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index d09db7f1b9..9bcf0215b7 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -1,12 +1,6 @@
 # -*- coding: utf-8 -*-
 """The ants module provides basic functions for interfacing with ants
     functions.
-
-   Change directory to provide relative paths for doctests
-   >>> import os
-   >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-   >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-   >>> os.chdir(datadir)
 """
 import csv
 import math
@@ -181,6 +175,8 @@ class AntsMotionCorr(ANTSCommand):
     Format and description of the affine motion correction parameters can be
     found in this PDF starting on page 555 section 3.9.16 AffineTransform:
     https://itk.org/ItkSoftwareGuide.pdf
+
+    https://github.com/stnava/ANTs/blob/master/Scripts/antsMotionCorrExample
     '''
     _cmd = 'antsMotionCorr'
     input_spec = AntsMotionCorrInputSpec
@@ -188,11 +184,20 @@ class AntsMotionCorr(ANTSCommand):
 
 
     def _gen_filename(self, name):
+        '''
+        If a fixed image is specified we are not going to be outputting
+        a newly created averaged image. The output flag for calls to 
+        antsMotionCorr with a fixed image have a value set for an average 
+        image. In all of the examples this value always matches the fixed 
+        image name.
+        '''
         if name == 'output_average_image':
             if _extant(self.inputs.fixed_image):
                 return self.inputs.fixed_image
             if not _extant(self.inputs.average_image):
                 raise ValueError("Either fixed_image or average_image must be defined")
+            if _extant(self.inputs.output_average_image):
+                return self.inputs.output_average_image
             pth, fname, ext = split_filename(self.inputs.average_image)
             new_fname = '{}{}{}'.format(fname, '_avg', ext)
             return os.path.join(pth, new_fname)

From 5c4193b6904bd6e074ecb290175d96ee4294807e Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 12:17:57 -0800
Subject: [PATCH 20/48] add examples of using AntsMotionCorr to take average of
 an image

---
 nipype/interfaces/ants/preprocess.py | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 9bcf0215b7..5634875c8d 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -149,6 +149,7 @@ class AntsMotionCorr(ANTSCommand):
     '''
     Examples
     -------
+
     >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
     >>> ants_mc = AntsMotionCorr()
     >>> ants_mc.inputs.metric_type = 'GC'
@@ -172,6 +173,18 @@ class AntsMotionCorr(ANTSCommand):
     >>> print(ants_mc.cmdline)
     antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
 
+    >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
+    >>> ants_avg = AntsMotionCorr()
+    >>> ants_avg.inputs.average_image = 'input.nii.gz'
+    >>> ants_avg.inputs.output_average_image = 'avg_out.nii.gz'
+    >>> print(ants_avg.cmdline)
+    antsMotionCorr -d 3 -a input.nii.gz -o avg_out.nii.gz
+
+    >>> ants_avg = AntsMotionCorr()
+    >>> ants_avg.inputs.average_image = 'input.nii.gz'
+    >>> print(ants_avg.cmdline)
+    antsMotionCorr -d 3 -a input.nii.gz -o input_avg.nii.gz
+
     Format and description of the affine motion correction parameters can be
     found in this PDF starting on page 555 section 3.9.16 AffineTransform:
     https://itk.org/ItkSoftwareGuide.pdf

From a2ca34e9ad525c570790726273903d4227ab6785 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 12:22:37 -0800
Subject: [PATCH 21/48] add note about lack of origin of rotation for
 motioncorrection conversion interface

---
 nipype/interfaces/ants/preprocess.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 5634875c8d..10027dca14 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -293,7 +293,10 @@ class AntsMatrixConversionOutputSpec(TraitedSpec):
 
 
 class AntsMatrixConversion(BaseInterface):
-    ''' Take antsMotionCorr motion output as input, convert to FSL style parameter files'''
+    '''
+    Take antsMotionCorr motion output as input, convert to FSL style
+    parameter files. Currently does not output origin of rotation.
+    '''
     input_spec = AntsMatrixConversionInputSpec
     output_spec = AntsMatrixConversionOutputSpec
 

From 6935720869e7f83d2cea213b1e8111e9ef46dfd0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 12:25:22 -0800
Subject: [PATCH 22/48] remove test wat

---
 nipype/interfaces/ants/preprocess.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 10027dca14..816e0338c5 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -163,7 +163,6 @@ class AntsMotionCorr(ANTSCommand):
     >>> ants_mc.inputs.n_images = 10
     >>> ants_mc.inputs.use_fixed_reference_image = True
     >>> ants_mc.inputs.use_scales_estimator = True
-    >>> ants_mc.inputs.output_average_image = 'wat'
     >>> ants_mc.inputs.output_warped_image = 'warped.nii.gz'
     >>> ants_mc.inputs.output_transform_prefix = 'motcorr'
     >>> ants_mc.inputs.transformation_model = 'Affine'

From 24d1e4e7c85582c4fa76b97f8c642a7f8c27cf0d Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 2 Mar 2017 12:42:22 -0800
Subject: [PATCH 23/48] Raise error if unable to format trasnformation model
 argument

---
 nipype/interfaces/ants/preprocess.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 816e0338c5..2904dbddf7 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -198,9 +198,9 @@ class AntsMotionCorr(ANTSCommand):
     def _gen_filename(self, name):
         '''
         If a fixed image is specified we are not going to be outputting
-        a newly created averaged image. The output flag for calls to 
-        antsMotionCorr with a fixed image have a value set for an average 
-        image. In all of the examples this value always matches the fixed 
+        a newly created averaged image. The output flag for calls to
+        antsMotionCorr with a fixed image have a value set for an average
+        image. In all of the examples this value always matches the fixed
         image name.
         '''
         if name == 'output_average_image':
@@ -248,7 +248,7 @@ def _format_transform(self):
                 and _extant(self.inputs.gradient_step_length)):
             return transform_str.format(self.inputs.transformation_model,
                                         self.inputs.gradient_step_length)
-        return " bad format "
+        raise ValueError("Unable to format transformation_model argument")
 
     def _format_output(self):
         if (_extant(self.inputs.output_transform_prefix)

From 42f85df33f6658b30bdf3fbcfaeb4e1dc7984154 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 3 Mar 2017 13:25:59 -0800
Subject: [PATCH 24/48] add write frame displacements arguments to
 antsmotioncorr. Also updated iterations, sigmas, and shrink factors, to be
 lists'

---
 nipype/interfaces/ants/preprocess.py          | 46 ++++++++++++++-----
 .../ants/tests/test_auto_AntsMotionCorr.py    | 10 +++-
 2 files changed, 44 insertions(+), 12 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 2904dbddf7..ffa148db98 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -103,19 +103,20 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     gradient_step_length = traits.Float(requires=['transformation_model'],
                                         desc='')
 
-    iterations = traits.Int(
-        argstr="-i %d",
-        desc="Specify the number of iterations at each level."
-    )
-    smoothing_sigmas = traits.Int(
-        argstr="-s %d",
-        desc="Specify the amount of smoothing at each level."
-    )
-    shrink_factors = traits.Int(
-        argstr="-f %d",
+    iterations = traits.List(traits.Int, argstr='-i %d', sep='x',
+                             desc="Specify the number of iterations at each level.")
+
+    smoothing_sigmas = traits.List(traits.Float, argstr='-s %f', sep='x',
+                                   desc="Specify the amount of smoothing at each level.")
+
+    shrink_factors = traits.List(
+        traits.Int,
+        argstr='-f %d',
+        sep='x',
         desc=("Specify the shrink factor for the virtual domain (typically "
               "the fixed image) at each level.")
     )
+
     n_images = traits.Int(
         argstr="-n %d",
         desc=("This option sets the number of images to use to construct the "
@@ -135,6 +136,21 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
         desc="use the scale estimator to control optimization."
     )
 
+    use_estimate_learning_rate_once = traits.Bool(
+        False,
+        argstr="-l %d",
+        desc=("turn on the option that lets you estimate the learning rate "
+              "step size only at the beginning of each level. Useful as a "
+              "second stage of fine-scale registration.")
+    )
+
+    write_displacement = traits.Bool(
+        False,
+        argstr="-w %d",
+        desc="Write the low-dimensional 3D transforms to a 4D displacement field"
+    )
+
+
 
 class AntsMotionCorrOutputSpec(TraitedSpec):
     '''Output spec for the antsMotionCorr command'''
@@ -144,6 +160,8 @@ class AntsMotionCorrOutputSpec(TraitedSpec):
     warped_image = File(desc="Outputs warped image")
     inverse_warped_image = File(desc="Outputs the inverse of the warped image")
     save_state = File(desc="The saved registration state to be restored")
+    displacement_field = File(desc=("4D displacement field that captures the "
+                                    "affine induced motion at each voxel"))
 
 class AntsMotionCorr(ANTSCommand):
     '''
@@ -261,7 +279,8 @@ def _format_output(self):
             )
         elif _extant(self.inputs.output_average_image):
             return "-o {}".format(self.inputs.output_average_image)
-        return ""
+        else:
+            raise ValueError("Unable to format output due to lack of inputs.")
 
     def _list_outputs(self):
         outputs = self._outputs().get()
@@ -278,6 +297,11 @@ def _list_outputs(self):
                 self.inputs.output_transform_prefix
             )
             outputs['composite_transform'] = os.path.abspath(fname)
+        if (_extant(self.inputs.write_displacement) and
+                _extant(self.inputs.output_transform_prefix) and
+                self.inputs.write_displacement is True):
+            fname = '{}Warp.nii.gz'.format(self.inputs.output_transform_prefix)
+            outputs['displacement_field'] = os.path.abspath(fname)
         return outputs
 
 class AntsMatrixConversionInputSpec(BaseInterfaceInputSpec):
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
index d340a437bf..886992cecd 100644
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
@@ -24,6 +24,7 @@ def test_AntsMotionCorr_inputs():
     usedefault=True,
     ),
     iterations=dict(argstr='-i %d',
+    sep='x',
     ),
     metric_type=dict(argstr='%s',
     ),
@@ -49,17 +50,23 @@ def test_AntsMotionCorr_inputs():
     sampling_strategy=dict(requires=['metric_type'],
     ),
     shrink_factors=dict(argstr='-f %d',
+    sep='x',
     ),
-    smoothing_sigmas=dict(argstr='-s %d',
+    smoothing_sigmas=dict(argstr='-s %f',
+    sep='x',
     ),
     terminal_output=dict(nohash=True,
     ),
     transformation_model=dict(argstr='%s',
     ),
+    use_estimate_learning_rate_once=dict(argstr='-l %d',
+    ),
     use_fixed_reference_image=dict(argstr='-u %d',
     ),
     use_scales_estimator=dict(argstr='-e %d',
     ),
+    write_displacement=dict(argstr='-w %d',
+    ),
     )
     inputs = AntsMotionCorr.input_spec()
 
@@ -71,6 +78,7 @@ def test_AntsMotionCorr_inputs():
 def test_AntsMotionCorr_outputs():
     output_map = dict(average_image=dict(),
     composite_transform=dict(),
+    displacement_field=dict(),
     inverse_composite_transform=dict(),
     inverse_warped_image=dict(),
     save_state=dict(),

From 23344890dce5b1d55ef896ca151d1595364f7b6d Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 3 Mar 2017 13:36:03 -0800
Subject: [PATCH 25/48] update list arguments to format as a string to properly
 account for specificed seperator

---
 nipype/interfaces/ants/preprocess.py                     | 6 +++---
 nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index ffa148db98..74cc65528c 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -103,15 +103,15 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
     gradient_step_length = traits.Float(requires=['transformation_model'],
                                         desc='')
 
-    iterations = traits.List(traits.Int, argstr='-i %d', sep='x',
+    iterations = traits.List(traits.Int, argstr='-i %s', sep='x',
                              desc="Specify the number of iterations at each level.")
 
-    smoothing_sigmas = traits.List(traits.Float, argstr='-s %f', sep='x',
+    smoothing_sigmas = traits.List(traits.Float, argstr='-s %s', sep='x',
                                    desc="Specify the amount of smoothing at each level.")
 
     shrink_factors = traits.List(
         traits.Int,
-        argstr='-f %d',
+        argstr='-f %s',
         sep='x',
         desc=("Specify the shrink factor for the virtual domain (typically "
               "the fixed image) at each level.")
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
index 886992cecd..2d526179fb 100644
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
+++ b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
@@ -23,7 +23,7 @@ def test_AntsMotionCorr_inputs():
     ignore_exception=dict(nohash=True,
     usedefault=True,
     ),
-    iterations=dict(argstr='-i %d',
+    iterations=dict(argstr='-i %s',
     sep='x',
     ),
     metric_type=dict(argstr='%s',
@@ -49,10 +49,10 @@ def test_AntsMotionCorr_inputs():
     ),
     sampling_strategy=dict(requires=['metric_type'],
     ),
-    shrink_factors=dict(argstr='-f %d',
+    shrink_factors=dict(argstr='-f %s',
     sep='x',
     ),
-    smoothing_sigmas=dict(argstr='-s %f',
+    smoothing_sigmas=dict(argstr='-s %s',
     sep='x',
     ),
     terminal_output=dict(nohash=True,

From 644ce4c7beaef291e022416a196feeb8d3aab8ac Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 3 Mar 2017 14:08:35 -0800
Subject: [PATCH 26/48] udpate antsmotioncorr example

---
 nipype/interfaces/ants/preprocess.py          |  9 +++---
 .../ants/tests/test_spec_AntsMotionCorr.py    | 31 +++++++++++++++++++
 2 files changed, 36 insertions(+), 4 deletions(-)
 create mode 100644 nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 74cc65528c..33f6aa7c8a 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -175,12 +175,13 @@ class AntsMotionCorr(ANTSCommand):
     >>> ants_mc.inputs.radius_or_bins = 1
     >>> ants_mc.inputs.sampling_strategy = "Random"
     >>> ants_mc.inputs.sampling_percentage = 0.05
-    >>> ants_mc.inputs.iterations = 10
-    >>> ants_mc.inputs.smoothing_sigmas = 0
-    >>> ants_mc.inputs.shrink_factors = 1
+    >>> ants_mc.inputs.iterations = [10,3]
+    >>> ants_mc.inputs.smoothing_sigmas = [0,0]
+    >>> ants_mc.inputs.shrink_factors = [1,1]
     >>> ants_mc.inputs.n_images = 10
     >>> ants_mc.inputs.use_fixed_reference_image = True
     >>> ants_mc.inputs.use_scales_estimator = True
+    >>> ants_mc.inputs.output_average_image = 'wat'
     >>> ants_mc.inputs.output_warped_image = 'warped.nii.gz'
     >>> ants_mc.inputs.output_transform_prefix = 'motcorr'
     >>> ants_mc.inputs.transformation_model = 'Affine'
@@ -188,7 +189,7 @@ class AntsMotionCorr(ANTSCommand):
     >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
     >>> ants_mc.inputs.moving_image = "input.nii.gz"
     >>> print(ants_mc.cmdline)
-    antsMotionCorr -d 3 -i 10 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1 -s 0 -t Affine[0.005] -u 1 -e 1
+    antsMotionCorr -d 3 -i 10x3 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1x1 -s 0.0x0.0 -t Affine[0.005] -u 1 -e 1
 
     >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
     >>> ants_avg = AntsMotionCorr()
diff --git a/nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py
new file mode 100644
index 0000000000..ae8119638d
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py
@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+from __future__ import division
+from nipype.interfaces.ants.preprocess import AntsMotionCorr
+
+def test_AntsMotionCorr_cmd():
+    ants_mc = AntsMotionCorr()
+    ants_mc.inputs.metric_type = 'GC'
+    ants_mc.inputs.metric_weight = 1
+    ants_mc.inputs.radius_or_bins = 1
+    ants_mc.inputs.sampling_strategy = "Random"
+    ants_mc.inputs.sampling_percentage = 0.05
+    ants_mc.inputs.iterations = [10, 3]
+    ants_mc.inputs.smoothing_sigmas = [0, 0]
+    ants_mc.inputs.shrink_factors = [1, 1]
+    ants_mc.inputs.n_images = 10
+    ants_mc.inputs.use_fixed_reference_image = True
+    ants_mc.inputs.use_scales_estimator = True
+    ants_mc.inputs.output_average_image = 'wat'
+    ants_mc.inputs.output_warped_image = 'warped.nii.gz'
+    ants_mc.inputs.output_transform_prefix = 'motcorr'
+    ants_mc.inputs.transformation_model = 'Affine'
+    ants_mc.inputs.gradient_step_length = 0.005
+    ants_mc.inputs.fixed_image = "average_image.nii.gz"
+    ants_mc.inputs.moving_image = "input.nii.gz"
+
+    expected_command = (
+        "antsMotionCorr -d 3 -i 10x3 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] "
+        "-n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1x1 -s 0.0x0.0 -t Affine[0.005] "
+        "-u 1 -e 1"
+    )
+    assert ants_mc.cmdline == expected_command

From 43f09135c7aa039e0e86bbc40b8ebf19fe7e01c6 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 10 Mar 2017 15:20:06 -0800
Subject: [PATCH 27/48] remove ants prefix from class names

---
 nipype/interfaces/ants/preprocess.py | 42 ++++++++++++++--------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 33f6aa7c8a..203db5bc0f 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -15,7 +15,7 @@
 def _extant(field):
     return (field is not None) and isdefined(field)
 
-class AntsMotionCorrStatsInputSpec(ANTSCommandInputSpec):
+class MotionCorrStatsInputSpec(ANTSCommandInputSpec):
     ''' Input spec for the antsMotionCorrStats command '''
     mask = File(argstr="-x %s", mandatory=True,
                 desc="compute displacements within specified mask.")
@@ -30,17 +30,17 @@ class AntsMotionCorrStatsInputSpec(ANTSCommandInputSpec):
     output_spatial_map = File(argstr='-s %s', hash_files=False,
                               desc="File to output displacement magnitude to.")
 
-class AntsMotionCorrStatsOutputSpec(TraitedSpec):
+class MotionCorrStatsOutputSpec(TraitedSpec):
     ''' Output spec for the antsMotionCorrStats command '''
     spatial_map = File(desc="output image of displacement magnitude", exists=True)
     output = File(desc="CSV file containg motion correction statistics", exists=True)
 
-class AntsMotionCorrStats(ANTSCommand):
+class MotionCorrStats(ANTSCommand):
     ''' Interface for the antsMotionCorrStats command '''
 
     _cmd = 'antsMotionCorrStats'
-    input_spec = AntsMotionCorrStatsInputSpec
-    output_spec = AntsMotionCorrStatsOutputSpec
+    input_spec = MotionCorrStatsInputSpec
+    output_spec = MotionCorrStatsOutputSpec
 
     def _gen_filename(self, name):
         if name == 'output':
@@ -57,7 +57,7 @@ def _list_outputs(self):
             outputs['output'] = os.path.abspath(self.inputs.output)
         return outputs
 
-class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
+class MotionCorrInputSpec(ANTSCommandInputSpec):
     '''Input spec for the antsMotionCorr command.'''
     dimension_desc = (
         "This option forces the image to be treated as a "
@@ -152,7 +152,7 @@ class AntsMotionCorrInputSpec(ANTSCommandInputSpec):
 
 
 
-class AntsMotionCorrOutputSpec(TraitedSpec):
+class MotionCorrOutputSpec(TraitedSpec):
     '''Output spec for the antsMotionCorr command'''
     average_image = File(exists=True, desc="Average of an image")
     composite_transform = File(desc="Composite transform file")
@@ -163,13 +163,13 @@ class AntsMotionCorrOutputSpec(TraitedSpec):
     displacement_field = File(desc=("4D displacement field that captures the "
                                     "affine induced motion at each voxel"))
 
-class AntsMotionCorr(ANTSCommand):
+class MotionCorr(ANTSCommand):
     '''
     Examples
     -------
 
-    >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
-    >>> ants_mc = AntsMotionCorr()
+    >>> from nipype.interfaces.ants.preprocess import MotionCorr
+    >>> ants_mc = MotionCorr()
     >>> ants_mc.inputs.metric_type = 'GC'
     >>> ants_mc.inputs.metric_weight = 1
     >>> ants_mc.inputs.radius_or_bins = 1
@@ -191,14 +191,14 @@ class AntsMotionCorr(ANTSCommand):
     >>> print(ants_mc.cmdline)
     antsMotionCorr -d 3 -i 10x3 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1x1 -s 0.0x0.0 -t Affine[0.005] -u 1 -e 1
 
-    >>> from nipype.interfaces.ants.preprocess import AntsMotionCorr
-    >>> ants_avg = AntsMotionCorr()
+    >>> from nipype.interfaces.ants.preprocess import MotionCorr
+    >>> ants_avg = MotionCorr()
     >>> ants_avg.inputs.average_image = 'input.nii.gz'
     >>> ants_avg.inputs.output_average_image = 'avg_out.nii.gz'
     >>> print(ants_avg.cmdline)
     antsMotionCorr -d 3 -a input.nii.gz -o avg_out.nii.gz
 
-    >>> ants_avg = AntsMotionCorr()
+    >>> ants_avg = MotionCorr()
     >>> ants_avg.inputs.average_image = 'input.nii.gz'
     >>> print(ants_avg.cmdline)
     antsMotionCorr -d 3 -a input.nii.gz -o input_avg.nii.gz
@@ -210,8 +210,8 @@ class AntsMotionCorr(ANTSCommand):
     https://github.com/stnava/ANTs/blob/master/Scripts/antsMotionCorrExample
     '''
     _cmd = 'antsMotionCorr'
-    input_spec = AntsMotionCorrInputSpec
-    output_spec = AntsMotionCorrOutputSpec
+    input_spec = MotionCorrInputSpec
+    output_spec = MotionCorrOutputSpec
 
 
     def _gen_filename(self, name):
@@ -246,7 +246,7 @@ def _format_arg(self, opt, spec, val):
         if opt == 'output_average_image':
             self.inputs.output_average_image = self._gen_filename("output_average_image")
             return self._format_output()
-        return super(AntsMotionCorr, self)._format_arg(opt, spec, val)
+        return super(MotionCorr, self)._format_arg(opt, spec, val)
 
     def _format_metric(self):
         metric_str = ("-m {metric_type}[{fixed_image},{moving_image},"
@@ -305,24 +305,24 @@ def _list_outputs(self):
             outputs['displacement_field'] = os.path.abspath(fname)
         return outputs
 
-class AntsMatrixConversionInputSpec(BaseInterfaceInputSpec):
+class Matrix2FSLParamsInputSpec(BaseInterfaceInputSpec):
     matrix = File(
         exists=True,
         desc='Motion crrection matrices to be converted into FSL style motion parameters',
         mandatory=True
     )
 
-class AntsMatrixConversionOutputSpec(TraitedSpec):
+class Matrix2FSLParamsOutputSpec(TraitedSpec):
     parameters = File(exists=True, desc="parameters to be output")
 
 
-class AntsMatrixConversion(BaseInterface):
+class Matrix2FSLParamsConversion(BaseInterface):
     '''
     Take antsMotionCorr motion output as input, convert to FSL style
     parameter files. Currently does not output origin of rotation.
     '''
-    input_spec = AntsMatrixConversionInputSpec
-    output_spec = AntsMatrixConversionOutputSpec
+    input_spec = Matrix2FSLParamsInputSpec
+    output_spec = Matrix2FSLParamsOutputSpec
 
     def _run_interface(self, runtime):
         in_fp = open(self.inputs.matrix)

From 2c3833de1219be92e730c5f06cb9c045710c0ee7 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 10 Mar 2017 15:24:23 -0800
Subject: [PATCH 28/48] update spec test for new class name

---
 ...{test_spec_AntsMotionCorr.py => test_spec_MotionCorr.py} | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)
 rename nipype/interfaces/ants/tests/{test_spec_AntsMotionCorr.py => test_spec_MotionCorr.py} (90%)

diff --git a/nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_spec_MotionCorr.py
similarity index 90%
rename from nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py
rename to nipype/interfaces/ants/tests/test_spec_MotionCorr.py
index ae8119638d..a5101eb934 100644
--- a/nipype/interfaces/ants/tests/test_spec_AntsMotionCorr.py
+++ b/nipype/interfaces/ants/tests/test_spec_MotionCorr.py
@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
 from __future__ import division
-from nipype.interfaces.ants.preprocess import AntsMotionCorr
+from nipype.interfaces.ants.preprocess import MotionCorr
 
-def test_AntsMotionCorr_cmd():
-    ants_mc = AntsMotionCorr()
+def test_MotionCorr_cmd():
+    ants_mc = MotionCorr()
     ants_mc.inputs.metric_type = 'GC'
     ants_mc.inputs.metric_weight = 1
     ants_mc.inputs.radius_or_bins = 1

From ebebf705cc2c24dbdf2329e041b5115392cf2e40 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 10 Mar 2017 15:25:42 -0800
Subject: [PATCH 29/48] update specs for new class names

---
 .../test_auto_Matrix2FSLParamsConversion.py   | 27 ++++++
 .../ants/tests/test_auto_MotionCorr.py        | 91 +++++++++++++++++++
 .../ants/tests/test_auto_MotionCorrStats.py   | 51 +++++++++++
 3 files changed, 169 insertions(+)
 create mode 100644 nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py
 create mode 100644 nipype/interfaces/ants/tests/test_auto_MotionCorr.py
 create mode 100644 nipype/interfaces/ants/tests/test_auto_MotionCorrStats.py

diff --git a/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py b/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py
new file mode 100644
index 0000000000..ff649a2c02
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py
@@ -0,0 +1,27 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import Matrix2FSLParamsConversion
+
+
+def test_Matrix2FSLParamsConversion_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    matrix=dict(mandatory=True,
+    ),
+    )
+    inputs = Matrix2FSLParamsConversion.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_Matrix2FSLParamsConversion_outputs():
+    output_map = dict(parameters=dict(),
+    )
+    outputs = Matrix2FSLParamsConversion.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_MotionCorr.py b/nipype/interfaces/ants/tests/test_auto_MotionCorr.py
new file mode 100644
index 0000000000..1099338673
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_MotionCorr.py
@@ -0,0 +1,91 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import MotionCorr
+
+
+def test_MotionCorr_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    average_image=dict(argstr='-a %s',
+    position=1,
+    ),
+    dimensionality=dict(argstr='-d %d',
+    position=0,
+    usedefault=True,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    fixed_image=dict(requires=['metric_type'],
+    ),
+    gradient_step_length=dict(requires=['transformation_model'],
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    iterations=dict(argstr='-i %s',
+    sep='x',
+    ),
+    metric_type=dict(argstr='%s',
+    ),
+    metric_weight=dict(requires=['metric_type'],
+    ),
+    moving_image=dict(requires=['metric_type'],
+    ),
+    n_images=dict(argstr='-n %d',
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    output_average_image=dict(argstr='%s',
+    genfile=True,
+    hash_files=False,
+    ),
+    output_transform_prefix=dict(),
+    output_warped_image=dict(),
+    radius_or_bins=dict(requires=['metric_type'],
+    ),
+    sampling_percentage=dict(requires=['metric_type'],
+    ),
+    sampling_strategy=dict(requires=['metric_type'],
+    ),
+    shrink_factors=dict(argstr='-f %s',
+    sep='x',
+    ),
+    smoothing_sigmas=dict(argstr='-s %s',
+    sep='x',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    transformation_model=dict(argstr='%s',
+    ),
+    use_estimate_learning_rate_once=dict(argstr='-l %d',
+    ),
+    use_fixed_reference_image=dict(argstr='-u %d',
+    ),
+    use_scales_estimator=dict(argstr='-e %d',
+    ),
+    write_displacement=dict(argstr='-w %d',
+    ),
+    )
+    inputs = MotionCorr.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MotionCorr_outputs():
+    output_map = dict(average_image=dict(),
+    composite_transform=dict(),
+    displacement_field=dict(),
+    inverse_composite_transform=dict(),
+    inverse_warped_image=dict(),
+    save_state=dict(),
+    warped_image=dict(),
+    )
+    outputs = MotionCorr.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_MotionCorrStats.py b/nipype/interfaces/ants/tests/test_auto_MotionCorrStats.py
new file mode 100644
index 0000000000..ecfe1653fb
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_auto_MotionCorrStats.py
@@ -0,0 +1,51 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..preprocess import MotionCorrStats
+
+
+def test_MotionCorrStats_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    framewise=dict(argstr='-f %d',
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    mask=dict(argstr='-x %s',
+    mandatory=True,
+    ),
+    moco=dict(argstr='-m %s',
+    mandatory=True,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    output=dict(argstr='-o %s',
+    genfile=True,
+    hash_files=False,
+    ),
+    output_spatial_map=dict(argstr='-s %s',
+    hash_files=False,
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = MotionCorrStats.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MotionCorrStats_outputs():
+    output_map = dict(output=dict(),
+    spatial_map=dict(),
+    )
+    outputs = MotionCorrStats.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

From 8b9c20a9f57f487aeb33f610544c398a6d691be8 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 10 Mar 2017 15:55:11 -0800
Subject: [PATCH 30/48] add test for Matrix2FSLParams

---
 nipype/interfaces/ants/preprocess.py          |  2 +-
 .../ants/tests/test_Matrix2FSLParams.py       | 34 +++++++++++++++++++
 2 files changed, 35 insertions(+), 1 deletion(-)
 create mode 100644 nipype/interfaces/ants/tests/test_Matrix2FSLParams.py

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 203db5bc0f..4e8e9c53e9 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -316,7 +316,7 @@ class Matrix2FSLParamsOutputSpec(TraitedSpec):
     parameters = File(exists=True, desc="parameters to be output")
 
 
-class Matrix2FSLParamsConversion(BaseInterface):
+class Matrix2FSLParams(BaseInterface):
     '''
     Take antsMotionCorr motion output as input, convert to FSL style
     parameter files. Currently does not output origin of rotation.
diff --git a/nipype/interfaces/ants/tests/test_Matrix2FSLParams.py b/nipype/interfaces/ants/tests/test_Matrix2FSLParams.py
new file mode 100644
index 0000000000..4b327e3819
--- /dev/null
+++ b/nipype/interfaces/ants/tests/test_Matrix2FSLParams.py
@@ -0,0 +1,34 @@
+import csv
+import os
+
+from nipype.interfaces.ants.preprocess import Matrix2FSLParams
+from nipype.utils.tmpdirs import InTemporaryDirectory
+from nipype.utils.filemanip import split_filename
+
+def test_Matrix2FSLParams():
+    with InTemporaryDirectory():
+        cwd = os.getcwd()
+        in_filename = os.path.join(cwd, 'in_file.csv')
+        fp = open(in_filename, 'w+')
+        fp.write("this line is ignored\n")
+        fp.write(
+            "0,-0.99918075422702,1.00028207678993,-7.41063731046199e-06,"
+            "3.93289649449106e-05,1.24969530535555e-05,1.00021114616063,"
+            "0.000233157514656132,-0.000195740079275366,-0.00033024846828514,"
+            "0.999495881936253,-0.0168301940330171,-0.0549722774931478,"
+            "0.202056708561567\n"
+        )
+        fp.close()
+        # m2p - matrix 2 parameters
+        m2p = Matrix2FSLParams()
+        m2p.inputs.matrix = in_filename
+        m2p.run()
+
+        pth, fname, _ = split_filename(in_filename)
+        params_fname = '{}{}'.format(fname, '.par')
+        params_fname = os.path.join(pth, params_fname)
+
+        params_fp = open(params_fname)
+        params_data = csv.reader(params_fp, delimiter=' ')
+        line = next(params_data)
+        assert len(line) == 6

From ebd5350d475ce92b9958603dd5eb17c4741e3f3d Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Fri, 10 Mar 2017 15:56:39 -0800
Subject: [PATCH 31/48] remove old auto tests

---
 .../ants/tests/test_auto_AntsMotionCorr.py    | 91 -------------------
 .../tests/test_auto_AntsMotionCorrStats.py    | 51 -----------
 .../test_auto_Matrix2FSLParamsConversion.py   | 27 ------
 3 files changed, 169 deletions(-)
 delete mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
 delete mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
 delete mode 100644 nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py

diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
deleted file mode 100644
index 2d526179fb..0000000000
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorr.py
+++ /dev/null
@@ -1,91 +0,0 @@
-# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from __future__ import unicode_literals
-from ..preprocess import AntsMotionCorr
-
-
-def test_AntsMotionCorr_inputs():
-    input_map = dict(args=dict(argstr='%s',
-    ),
-    average_image=dict(argstr='-a %s',
-    position=1,
-    ),
-    dimensionality=dict(argstr='-d %d',
-    position=0,
-    usedefault=True,
-    ),
-    environ=dict(nohash=True,
-    usedefault=True,
-    ),
-    fixed_image=dict(requires=['metric_type'],
-    ),
-    gradient_step_length=dict(requires=['transformation_model'],
-    ),
-    ignore_exception=dict(nohash=True,
-    usedefault=True,
-    ),
-    iterations=dict(argstr='-i %s',
-    sep='x',
-    ),
-    metric_type=dict(argstr='%s',
-    ),
-    metric_weight=dict(requires=['metric_type'],
-    ),
-    moving_image=dict(requires=['metric_type'],
-    ),
-    n_images=dict(argstr='-n %d',
-    ),
-    num_threads=dict(nohash=True,
-    usedefault=True,
-    ),
-    output_average_image=dict(argstr='%s',
-    genfile=True,
-    hash_files=False,
-    ),
-    output_transform_prefix=dict(),
-    output_warped_image=dict(),
-    radius_or_bins=dict(requires=['metric_type'],
-    ),
-    sampling_percentage=dict(requires=['metric_type'],
-    ),
-    sampling_strategy=dict(requires=['metric_type'],
-    ),
-    shrink_factors=dict(argstr='-f %s',
-    sep='x',
-    ),
-    smoothing_sigmas=dict(argstr='-s %s',
-    sep='x',
-    ),
-    terminal_output=dict(nohash=True,
-    ),
-    transformation_model=dict(argstr='%s',
-    ),
-    use_estimate_learning_rate_once=dict(argstr='-l %d',
-    ),
-    use_fixed_reference_image=dict(argstr='-u %d',
-    ),
-    use_scales_estimator=dict(argstr='-e %d',
-    ),
-    write_displacement=dict(argstr='-w %d',
-    ),
-    )
-    inputs = AntsMotionCorr.input_spec()
-
-    for key, metadata in list(input_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(inputs.traits()[key], metakey) == value
-
-
-def test_AntsMotionCorr_outputs():
-    output_map = dict(average_image=dict(),
-    composite_transform=dict(),
-    displacement_field=dict(),
-    inverse_composite_transform=dict(),
-    inverse_warped_image=dict(),
-    save_state=dict(),
-    warped_image=dict(),
-    )
-    outputs = AntsMotionCorr.output_spec()
-
-    for key, metadata in list(output_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py b/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
deleted file mode 100644
index e81fb4f95d..0000000000
--- a/nipype/interfaces/ants/tests/test_auto_AntsMotionCorrStats.py
+++ /dev/null
@@ -1,51 +0,0 @@
-# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from __future__ import unicode_literals
-from ..preprocess import AntsMotionCorrStats
-
-
-def test_AntsMotionCorrStats_inputs():
-    input_map = dict(args=dict(argstr='%s',
-    ),
-    environ=dict(nohash=True,
-    usedefault=True,
-    ),
-    framewise=dict(argstr='-f %d',
-    ),
-    ignore_exception=dict(nohash=True,
-    usedefault=True,
-    ),
-    mask=dict(argstr='-x %s',
-    mandatory=True,
-    ),
-    moco=dict(argstr='-m %s',
-    mandatory=True,
-    ),
-    num_threads=dict(nohash=True,
-    usedefault=True,
-    ),
-    output=dict(argstr='-o %s',
-    genfile=True,
-    hash_files=False,
-    ),
-    output_spatial_map=dict(argstr='-s %s',
-    hash_files=False,
-    ),
-    terminal_output=dict(nohash=True,
-    ),
-    )
-    inputs = AntsMotionCorrStats.input_spec()
-
-    for key, metadata in list(input_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(inputs.traits()[key], metakey) == value
-
-
-def test_AntsMotionCorrStats_outputs():
-    output_map = dict(output=dict(),
-    spatial_map=dict(),
-    )
-    outputs = AntsMotionCorrStats.output_spec()
-
-    for key, metadata in list(output_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(outputs.traits()[key], metakey) == value
diff --git a/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py b/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py
deleted file mode 100644
index ff649a2c02..0000000000
--- a/nipype/interfaces/ants/tests/test_auto_Matrix2FSLParamsConversion.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from __future__ import unicode_literals
-from ..preprocess import Matrix2FSLParamsConversion
-
-
-def test_Matrix2FSLParamsConversion_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
-    usedefault=True,
-    ),
-    matrix=dict(mandatory=True,
-    ),
-    )
-    inputs = Matrix2FSLParamsConversion.input_spec()
-
-    for key, metadata in list(input_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(inputs.traits()[key], metakey) == value
-
-
-def test_Matrix2FSLParamsConversion_outputs():
-    output_map = dict(parameters=dict(),
-    )
-    outputs = Matrix2FSLParamsConversion.output_spec()
-
-    for key, metadata in list(output_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(outputs.traits()[key], metakey) == value

From 82877444c3bac8457f9801786d8ea58112ecd289 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 13 Mar 2017 09:36:21 -0700
Subject: [PATCH 32/48] add preprocess functions to init

---
 nipype/interfaces/ants/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nipype/interfaces/ants/__init__.py b/nipype/interfaces/ants/__init__.py
index 3bb83b3df9..faafcea2b3 100644
--- a/nipype/interfaces/ants/__init__.py
+++ b/nipype/interfaces/ants/__init__.py
@@ -3,6 +3,8 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
 """Top-level namespace for ants."""
+# Preprocessing Programs
+from .preprocess import Matrix2FSLParams, MotionCorr, MotionCorrStats
 
 # Registraiton programs
 from .registration import ANTS, Registration

From deba31ae286a878bc0b04b04225180b058d81073 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 13 Mar 2017 09:37:35 -0700
Subject: [PATCH 33/48] remove unnecessary _extant function

---
 nipype/interfaces/ants/preprocess.py | 39 +++++++++++++---------------
 1 file changed, 18 insertions(+), 21 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 4e8e9c53e9..0265287931 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -12,9 +12,6 @@
 from ...utils.filemanip import split_filename
 
 
-def _extant(field):
-    return (field is not None) and isdefined(field)
-
 class MotionCorrStatsInputSpec(ANTSCommandInputSpec):
     ''' Input spec for the antsMotionCorrStats command '''
     mask = File(argstr="-x %s", mandatory=True,
@@ -49,11 +46,11 @@ def _gen_filename(self, name):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        if _extant(self.inputs.output_spatial_map):
+        if isdefined(self.inputs.output_spatial_map):
             outputs['spatial_map'] = (
                 os.path.abspath(self.inputs.output_spatial_map)
             )
-        if _extant(self.inputs.output):
+        if isdefined(self.inputs.output):
             outputs['output'] = os.path.abspath(self.inputs.output)
         return outputs
 
@@ -223,16 +220,16 @@ def _gen_filename(self, name):
         image name.
         '''
         if name == 'output_average_image':
-            if _extant(self.inputs.fixed_image):
+            if isdefined(self.inputs.fixed_image):
                 return self.inputs.fixed_image
-            if not _extant(self.inputs.average_image):
+            if not isdefined(self.inputs.average_image):
                 raise ValueError("Either fixed_image or average_image must be defined")
-            if _extant(self.inputs.output_average_image):
+            if isdefined(self.inputs.output_average_image):
                 return self.inputs.output_average_image
             pth, fname, ext = split_filename(self.inputs.average_image)
             new_fname = '{}{}{}'.format(fname, '_avg', ext)
             return os.path.join(pth, new_fname)
-        if name == 'ouput_warped_image' and _extant(self.inputs.fixed_image):
+        if name == 'ouput_warped_image' and isdefined(self.inputs.fixed_image):
             pth, fname, ext = split_filename(self.inputs.fixed_image)
             new_fname = '{}{}{}'.format(fname, '_warped', ext)
             return os.path.join(pth, new_fname)
@@ -257,49 +254,49 @@ def _format_metric(self):
                        "metric_weight", "radius_or_bins", "sampling_strategy",
                        "sampling_percentage"]
         for metric_arg in metric_args:
-            if _extant(getattr(self.inputs, metric_arg)):
+            if isdefined(getattr(self.inputs, metric_arg)):
                 format_args[metric_arg] = getattr(self.inputs, metric_arg)
         return metric_str.format(**format_args)
 
     def _format_transform(self):
         transform_str = "-t {}[{}]"
-        if (_extant(self.inputs.transformation_model)
-                and _extant(self.inputs.gradient_step_length)):
+        if (isdefined(self.inputs.transformation_model)
+                and isdefined(self.inputs.gradient_step_length)):
             return transform_str.format(self.inputs.transformation_model,
                                         self.inputs.gradient_step_length)
         raise ValueError("Unable to format transformation_model argument")
 
     def _format_output(self):
-        if (_extant(self.inputs.output_transform_prefix)
-                and _extant(self.inputs.output_warped_image)
-                and _extant(self.inputs.output_average_image)):
+        if (isdefined(self.inputs.output_transform_prefix)
+                and isdefined(self.inputs.output_warped_image)
+                and isdefined(self.inputs.output_average_image)):
             return "-o [{},{},{}]".format(
                 self.inputs.output_transform_prefix,
                 self.inputs.output_warped_image,
                 self.inputs.output_average_image
             )
-        elif _extant(self.inputs.output_average_image):
+        elif isdefined(self.inputs.output_average_image):
             return "-o {}".format(self.inputs.output_average_image)
         else:
             raise ValueError("Unable to format output due to lack of inputs.")
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        if _extant(self.inputs.output_average_image):
+        if isdefined(self.inputs.output_average_image):
             outputs['average_image'] = (
                 os.path.abspath(self.inputs.output_average_image)
             )
-        if _extant(self.inputs.output_warped_image):
+        if isdefined(self.inputs.output_warped_image):
             outputs['warped_image'] = (
                 os.path.abspath(self.inputs.output_warped_image)
             )
-        if _extant(self.inputs.output_transform_prefix):
+        if isdefined(self.inputs.output_transform_prefix):
             fname = '{}MOCOparams.csv'.format(
                 self.inputs.output_transform_prefix
             )
             outputs['composite_transform'] = os.path.abspath(fname)
-        if (_extant(self.inputs.write_displacement) and
-                _extant(self.inputs.output_transform_prefix) and
+        if (isdefined(self.inputs.write_displacement) and
+                isdefined(self.inputs.output_transform_prefix) and
                 self.inputs.write_displacement is True):
             fname = '{}Warp.nii.gz'.format(self.inputs.output_transform_prefix)
             outputs['displacement_field'] = os.path.abspath(fname)

From 045e798cbe660ae4105ada8e2c8df9b0a94b3c74 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 13 Mar 2017 09:38:50 -0700
Subject: [PATCH 34/48] remove old auto test

---
 .../tests/test_auto_AntsMatrixConversion.py   | 27 -------------------
 1 file changed, 27 deletions(-)
 delete mode 100644 nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py

diff --git a/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py b/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py
deleted file mode 100644
index f7ecb64d2b..0000000000
--- a/nipype/interfaces/ants/tests/test_auto_AntsMatrixConversion.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
-from __future__ import unicode_literals
-from ..preprocess import AntsMatrixConversion
-
-
-def test_AntsMatrixConversion_inputs():
-    input_map = dict(ignore_exception=dict(nohash=True,
-    usedefault=True,
-    ),
-    matrix=dict(mandatory=True,
-    ),
-    )
-    inputs = AntsMatrixConversion.input_spec()
-
-    for key, metadata in list(input_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(inputs.traits()[key], metakey) == value
-
-
-def test_AntsMatrixConversion_outputs():
-    output_map = dict(parameters=dict(),
-    )
-    outputs = AntsMatrixConversion.output_spec()
-
-    for key, metadata in list(output_map.items()):
-        for metakey, value in list(metadata.items()):
-            assert getattr(outputs.traits()[key], metakey) == value

From c5e90a191eb0bb6060d1cd6c1e21f0fde03dbfd1 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 10:56:45 -0700
Subject: [PATCH 35/48] switch matrix conversion to use nibabel

---
 nipype/interfaces/ants/preprocess.py | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 0265287931..666ecf64c0 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -3,9 +3,11 @@
     functions.
 """
 import csv
-import math
 import os
 
+from nibabel.eulerangles import mat2euler
+import numpy
+
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
                     traits, isdefined, Str)
 from .base import ANTSCommand, ANTSCommandInputSpec
@@ -330,12 +332,13 @@ def _run_interface(self, runtime):
         next(in_data)
 
         for x in in_data:
-            t1 = math.atan2(float(x[7]), float(x[10]))
-            c2 = math.sqrt((float(x[2]) * float(x[2])) + (float(x[3]) * float(x[3])))
-            t2 = math.atan2(-float(x[4]), c2)
-            t3 = math.atan2(float(x[3]), float(x[2]))
+            mat = numpy.zeroes((3, 3))
+            mat[0] = [x[2], x[3], x[4]]
+            mat[1] = [x[5], x[6], x[7]]
+            mat[2] = [x[8], x[9], x[10]]
+            param_z, param_y, param_x = mat2euler(mat)
             parameters = "{:.8f} {:.8f} {:.8f} {:.8f} {:.8f} {:.8f}"
-            pars.append(parameters.format(t1, t2, t3, float(x[11]), float(x[12]),
+            pars.append(parameters.format(param_x, param_y, param_z, float(x[11]), float(x[12]),
                                           float(x[13])))
 
         pth, fname, _ = split_filename(self.inputs.matrix)

From 95313e14a0b541bf8de51c3746b5f978126e9154 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 12:16:16 -0700
Subject: [PATCH 36/48] update matrix conversion names, fix typo, make output
 file naming simpler

---
 nipype/interfaces/ants/preprocess.py          | 36 ++++++++-----------
 ...Params.py => test_MotionCorr2FSLParams.py} |  8 ++---
 2 files changed, 19 insertions(+), 25 deletions(-)
 rename nipype/interfaces/ants/tests/{test_Matrix2FSLParams.py => test_MotionCorr2FSLParams.py} (85%)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 666ecf64c0..4aa3ff8ee4 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -304,27 +304,29 @@ def _list_outputs(self):
             outputs['displacement_field'] = os.path.abspath(fname)
         return outputs
 
-class Matrix2FSLParamsInputSpec(BaseInterfaceInputSpec):
-    matrix = File(
+class MotionCorr2FSLParamsInputSpec(BaseInterfaceInputSpec):
+    ants_matrix = File(
         exists=True,
-        desc='Motion crrection matrices to be converted into FSL style motion parameters',
+        desc='Motion correction matrices to be converted into FSL style motion parameters',
         mandatory=True
     )
+    fsl_params = File(name_template='%s.par', name_source='ants_matrix',
+                      desc='FSL parameter file')
 
-class Matrix2FSLParamsOutputSpec(TraitedSpec):
-    parameters = File(exists=True, desc="parameters to be output")
+class MotionCorr2FSLParamsOutputSpec(TraitedSpec):
+    fsl_params = File(exists=True, desc="FSL parameters file to be output")
 
 
-class Matrix2FSLParams(BaseInterface):
+class MotionCorr2FSLParams(BaseInterface):
     '''
-    Take antsMotionCorr motion output as input, convert to FSL style
+    Take antsMotionCorr motion output as input, convert to FSL-style
     parameter files. Currently does not output origin of rotation.
     '''
-    input_spec = Matrix2FSLParamsInputSpec
-    output_spec = Matrix2FSLParamsOutputSpec
+    input_spec = MotionCorr2FSLParamsInputSpec
+    output_spec = MotionCorr2FSLParamsOutputSpec
 
     def _run_interface(self, runtime):
-        in_fp = open(self.inputs.matrix)
+        in_fp = open(self.inputs.ants_matrix)
         in_data = csv.reader(in_fp)
         pars = []
 
@@ -341,18 +343,10 @@ def _run_interface(self, runtime):
             pars.append(parameters.format(param_x, param_y, param_z, float(x[11]), float(x[12]),
                                           float(x[13])))
 
-        pth, fname, _ = split_filename(self.inputs.matrix)
+        pth, fname, _ = split_filename(self.inputs.ants_matrix)
         new_fname = '{}{}'.format(fname, '.par')
-        parameters = os.path.join(pth, new_fname)
-        with open(parameters, mode='wt') as out_fp:
+        fsl_params = os.path.join(pth, new_fname)
+        with open(fsl_params, mode='wt') as out_fp:
             out_fp.write('\n'.join(pars))
         in_fp.close()
         return runtime
-
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        pth, fname, _ = split_filename(self.inputs.matrix)
-        new_fname = '{}{}'.format(fname, '.par')
-        out_file = os.path.join(pth, new_fname)
-        outputs["parameters"] = out_file
-        return outputs
diff --git a/nipype/interfaces/ants/tests/test_Matrix2FSLParams.py b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
similarity index 85%
rename from nipype/interfaces/ants/tests/test_Matrix2FSLParams.py
rename to nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
index 4b327e3819..e055542da0 100644
--- a/nipype/interfaces/ants/tests/test_Matrix2FSLParams.py
+++ b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
@@ -1,11 +1,11 @@
 import csv
 import os
 
-from nipype.interfaces.ants.preprocess import Matrix2FSLParams
+from nipype.interfaces.ants.preprocess import MotionCorr2FSLParams
 from nipype.utils.tmpdirs import InTemporaryDirectory
 from nipype.utils.filemanip import split_filename
 
-def test_Matrix2FSLParams():
+def test_MotionCorr2FSLParams():
     with InTemporaryDirectory():
         cwd = os.getcwd()
         in_filename = os.path.join(cwd, 'in_file.csv')
@@ -20,8 +20,8 @@ def test_Matrix2FSLParams():
         )
         fp.close()
         # m2p - matrix 2 parameters
-        m2p = Matrix2FSLParams()
-        m2p.inputs.matrix = in_filename
+        m2p = MotionCorr2FSLParams()
+        m2p.inputs.ants_matrix = in_filename
         m2p.run()
 
         pth, fname, _ = split_filename(in_filename)

From 5c1e3f68193c5cffc4f50d6fbe603a56f6e3b8aa Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 12:59:38 -0700
Subject: [PATCH 37/48]  update init to match new names in preprocess

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

diff --git a/nipype/interfaces/ants/__init__.py b/nipype/interfaces/ants/__init__.py
index faafcea2b3..ed7e7dbbce 100644
--- a/nipype/interfaces/ants/__init__.py
+++ b/nipype/interfaces/ants/__init__.py
@@ -4,7 +4,7 @@
 
 """Top-level namespace for ants."""
 # Preprocessing Programs
-from .preprocess import Matrix2FSLParams, MotionCorr, MotionCorrStats
+from .preprocess import MotionCorr2FSLParams, MotionCorr, MotionCorrStats
 
 # Registraiton programs
 from .registration import ANTS, Registration

From 01bc07d7ccaff39d15a7d7f2c04058825d6d6176 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 13:05:57 -0700
Subject: [PATCH 38/48] fix spelling mistake

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

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 4aa3ff8ee4..0646f21283 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -334,7 +334,7 @@ def _run_interface(self, runtime):
         next(in_data)
 
         for x in in_data:
-            mat = numpy.zeroes((3, 3))
+            mat = numpy.zeros((3, 3))
             mat[0] = [x[2], x[3], x[4]]
             mat[1] = [x[5], x[6], x[7]]
             mat[2] = [x[8], x[9], x[10]]

From 32968cd8cda1e0def2bcb68dd878c56ca9c67827 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 13:11:33 -0700
Subject: [PATCH 39/48] still need _list_outputs

---
 nipype/interfaces/ants/preprocess.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 0646f21283..458f41f955 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -310,8 +310,6 @@ class MotionCorr2FSLParamsInputSpec(BaseInterfaceInputSpec):
         desc='Motion correction matrices to be converted into FSL style motion parameters',
         mandatory=True
     )
-    fsl_params = File(name_template='%s.par', name_source='ants_matrix',
-                      desc='FSL parameter file')
 
 class MotionCorr2FSLParamsOutputSpec(TraitedSpec):
     fsl_params = File(exists=True, desc="FSL parameters file to be output")
@@ -350,3 +348,11 @@ def _run_interface(self, runtime):
             out_fp.write('\n'.join(pars))
         in_fp.close()
         return runtime
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        pth, fname, _ = split_filename(self.inputs.matrix)
+        new_fname = '{}{}'.format(fname, '.par')
+        out_file = os.path.join(pth, new_fname)
+        outputs["parameters"] = out_file
+        return outputs

From ab74434b2a1879cf957e00c0fb185f864e031282 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Wed, 15 Mar 2017 13:14:51 -0700
Subject: [PATCH 40/48]  correct input and output names in list_outputs

---
 nipype/interfaces/ants/preprocess.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 458f41f955..aaa5f9efe0 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -351,8 +351,8 @@ def _run_interface(self, runtime):
 
     def _list_outputs(self):
         outputs = self._outputs().get()
-        pth, fname, _ = split_filename(self.inputs.matrix)
+        pth, fname, _ = split_filename(self.inputs.ants_matrix)
         new_fname = '{}{}'.format(fname, '.par')
         out_file = os.path.join(pth, new_fname)
-        outputs["parameters"] = out_file
+        outputs["fsl_params"] = out_file
         return outputs

From 7401ad0e59a45abbbdb65c5a8aeb6fc801fdf932 Mon Sep 17 00:00:00 2001
From: Ross Blair <rblair2@stanford.edu>
Date: Thu, 16 Mar 2017 13:35:51 -0700
Subject: [PATCH 41/48] update motioncorr2fslparams test to check to see if the
 original and converted parameters are close in value

---
 .../ants/tests/test_MotionCorr2FSLParams.py   | 43 +++++++++++++------
 1 file changed, 31 insertions(+), 12 deletions(-)

diff --git a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
index e055542da0..4e577d128b 100644
--- a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
+++ b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
@@ -1,34 +1,53 @@
-import csv
 import os
 
+import numpy
+
 from nipype.interfaces.ants.preprocess import MotionCorr2FSLParams
+from nipype.interfaces.fsl.utils import AvScale
 from nipype.utils.tmpdirs import InTemporaryDirectory
 from nipype.utils.filemanip import split_filename
 
 def test_MotionCorr2FSLParams():
     with InTemporaryDirectory():
         cwd = os.getcwd()
+        fsl_mat_fname = "fsl_style.mat"
+        fp = open(fsl_mat_fname, 'w+')
+        fp.write(
+            "1.000000 0.000000 -0.000935 0.062539\n"
+            "0.000001 0.999999 0.001470 -0.162467\n"
+            "0.000935 -0.001470 0.999999 -0.279038\n"
+            "0.000000 0.000000 0.000000 1.000000\n"
+        )
+        fp.close()
+
         in_filename = os.path.join(cwd, 'in_file.csv')
         fp = open(in_filename, 'w+')
         fp.write("this line is ignored\n")
         fp.write(
-            "0,-0.99918075422702,1.00028207678993,-7.41063731046199e-06,"
-            "3.93289649449106e-05,1.24969530535555e-05,1.00021114616063,"
-            "0.000233157514656132,-0.000195740079275366,-0.00033024846828514,"
-            "0.999495881936253,-0.0168301940330171,-0.0549722774931478,"
-            "0.202056708561567\n"
+            "0,-0.99918075422702,1.000000,0.000000,-0.000935,0.000001,"
+            "0.999999,0.001470,0.000935,-0.001470,0.999999,-0.279038,0.062539,"
+            "-0.162467,-0.279038\n"
         )
         fp.close()
+
         # m2p - matrix 2 parameters
         m2p = MotionCorr2FSLParams()
         m2p.inputs.ants_matrix = in_filename
         m2p.run()
 
         pth, fname, _ = split_filename(in_filename)
-        params_fname = '{}{}'.format(fname, '.par')
-        params_fname = os.path.join(pth, params_fname)
+        conv_params_fname = '{}{}'.format(fname, '.par')
+        conv_params_fname = os.path.join(pth, conv_params_fname)
+
+        avscale = AvScale()
+        avscale.inputs.all_param = True
+        avscale.inputs.mat_file = fsl_mat_fname
+        avscale.run()
+        avscale_out = avscale.aggregate_outputs()
+        orig_params = []
+        orig_params.extend(avscale_out.rot_angles)
+        orig_params.extend(avscale_out.translations)
+        conv_params = numpy.genfromtext(conv_params_fname, delimeter=' ')
+        comp = numpy.isclose(conv_params, orig_params)
 
-        params_fp = open(params_fname)
-        params_data = csv.reader(params_fp, delimiter=' ')
-        line = next(params_data)
-        assert len(line) == 6
+        assert(False not in comp)

From 56ebd4a3c08e815c778ce16f49d3ff95cd342fce Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 16 Mar 2017 15:01:29 -0700
Subject: [PATCH 42/48] switch file operatations to use numpy in
 test_MotionCorr2FSLParams

---
 .../ants/tests/test_MotionCorr2FSLParams.py   | 32 +++++++++----------
 1 file changed, 16 insertions(+), 16 deletions(-)

diff --git a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
index 4e577d128b..9f7765aa2f 100644
--- a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
+++ b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
@@ -11,24 +11,24 @@ def test_MotionCorr2FSLParams():
     with InTemporaryDirectory():
         cwd = os.getcwd()
         fsl_mat_fname = "fsl_style.mat"
-        fp = open(fsl_mat_fname, 'w+')
-        fp.write(
-            "1.000000 0.000000 -0.000935 0.062539\n"
-            "0.000001 0.999999 0.001470 -0.162467\n"
-            "0.000935 -0.001470 0.999999 -0.279038\n"
-            "0.000000 0.000000 0.000000 1.000000\n"
+        fsl_mat = numpy.array(
+            [
+                [1.000000, 0.000000, -0.000935, 0.062539],
+                [0.000001, 0.999999, 0.001470, -0.162467],
+                [0.000935, -0.001470, 0.999999, -0.279038],
+                [0.000000, 0.000000, 0.000000, 1.000000]
+            ]
         )
-        fp.close()
+        numpy.savetxt(fsl_mat_fname, fsl_mat, delimiter=' ')
 
         in_filename = os.path.join(cwd, 'in_file.csv')
-        fp = open(in_filename, 'w+')
-        fp.write("this line is ignored\n")
-        fp.write(
-            "0,-0.99918075422702,1.000000,0.000000,-0.000935,0.000001,"
-            "0.999999,0.001470,0.000935,-0.001470,0.999999,-0.279038,0.062539,"
-            "-0.162467,-0.279038\n"
-        )
-        fp.close()
+        ants_mat = numpy.array([
+            0, -0.99918075422702, 1.000000, 0.000000, -0.000935, 0.000001,
+            0.999999, 0.001470, 0.000935, -0.001470, 0.999999, -0.279038,
+            0.062539, -0.162467, -0.279038
+        ])
+        numpy.savetxt(in_filename, ants_mat, delimiter=',',
+                      header="this line is ignored")
 
         # m2p - matrix 2 parameters
         m2p = MotionCorr2FSLParams()
@@ -47,7 +47,7 @@ def test_MotionCorr2FSLParams():
         orig_params = []
         orig_params.extend(avscale_out.rot_angles)
         orig_params.extend(avscale_out.translations)
-        conv_params = numpy.genfromtext(conv_params_fname, delimeter=' ')
+        conv_params = numpy.genfromtxt(conv_params_fname, delimiter=' ')
         comp = numpy.isclose(conv_params, orig_params)
 
         assert(False not in comp)

From a13a7dd1716704cb9ff5a555d07fbbdad8d9cfa0 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 16 Mar 2017 15:08:31 -0700
Subject: [PATCH 43/48] switch file operations in MotionCorr2FslParams to use
 numpy savetxt

---
 nipype/interfaces/ants/preprocess.py | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index aaa5f9efe0..cb70c25783 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -343,10 +343,9 @@ def _run_interface(self, runtime):
 
         pth, fname, _ = split_filename(self.inputs.ants_matrix)
         new_fname = '{}{}'.format(fname, '.par')
-        fsl_params = os.path.join(pth, new_fname)
-        with open(fsl_params, mode='wt') as out_fp:
-            out_fp.write('\n'.join(pars))
-        in_fp.close()
+        fsl_params_fname = os.path.join(pth, new_fname)
+        fsl_params = numpy.array(pars)
+        numpy.savetxt(fsl_params_fname, fsl_params, delimiter=' ')
         return runtime
 
     def _list_outputs(self):

From 696aa4a334860088d70255fe5bc6829c598d23bc Mon Sep 17 00:00:00 2001
From: Ross Blair <rblair2@stanford.edu>
Date: Thu, 16 Mar 2017 16:36:10 -0700
Subject: [PATCH 44/48] have newly generated parameters be saved as arrays not
 strings so that output via numpy works as expected

---
 nipype/interfaces/ants/preprocess.py          |  5 +-
 .../ants/tests/test_MotionCorr2FSLParams.py   | 87 ++++++++++---------
 2 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index cb70c25783..07c00e978d 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -337,9 +337,8 @@ def _run_interface(self, runtime):
             mat[1] = [x[5], x[6], x[7]]
             mat[2] = [x[8], x[9], x[10]]
             param_z, param_y, param_x = mat2euler(mat)
-            parameters = "{:.8f} {:.8f} {:.8f} {:.8f} {:.8f} {:.8f}"
-            pars.append(parameters.format(param_x, param_y, param_z, float(x[11]), float(x[12]),
-                                          float(x[13])))
+            pars.append([param_x, param_y, param_z, float(x[11]), float(x[12]),
+                        float(x[13])])
 
         pth, fname, _ = split_filename(self.inputs.ants_matrix)
         new_fname = '{}{}'.format(fname, '.par')
diff --git a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
index 9f7765aa2f..ce24522c6f 100644
--- a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
+++ b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
@@ -8,46 +8,47 @@
 from nipype.utils.filemanip import split_filename
 
 def test_MotionCorr2FSLParams():
-    with InTemporaryDirectory():
-        cwd = os.getcwd()
-        fsl_mat_fname = "fsl_style.mat"
-        fsl_mat = numpy.array(
-            [
-                [1.000000, 0.000000, -0.000935, 0.062539],
-                [0.000001, 0.999999, 0.001470, -0.162467],
-                [0.000935, -0.001470, 0.999999, -0.279038],
-                [0.000000, 0.000000, 0.000000, 1.000000]
-            ]
-        )
-        numpy.savetxt(fsl_mat_fname, fsl_mat, delimiter=' ')
-
-        in_filename = os.path.join(cwd, 'in_file.csv')
-        ants_mat = numpy.array([
-            0, -0.99918075422702, 1.000000, 0.000000, -0.000935, 0.000001,
-            0.999999, 0.001470, 0.000935, -0.001470, 0.999999, -0.279038,
-            0.062539, -0.162467, -0.279038
-        ])
-        numpy.savetxt(in_filename, ants_mat, delimiter=',',
-                      header="this line is ignored")
-
-        # m2p - matrix 2 parameters
-        m2p = MotionCorr2FSLParams()
-        m2p.inputs.ants_matrix = in_filename
-        m2p.run()
-
-        pth, fname, _ = split_filename(in_filename)
-        conv_params_fname = '{}{}'.format(fname, '.par')
-        conv_params_fname = os.path.join(pth, conv_params_fname)
-
-        avscale = AvScale()
-        avscale.inputs.all_param = True
-        avscale.inputs.mat_file = fsl_mat_fname
-        avscale.run()
-        avscale_out = avscale.aggregate_outputs()
-        orig_params = []
-        orig_params.extend(avscale_out.rot_angles)
-        orig_params.extend(avscale_out.translations)
-        conv_params = numpy.genfromtxt(conv_params_fname, delimiter=' ')
-        comp = numpy.isclose(conv_params, orig_params)
-
-        assert(False not in comp)
+    #with InTemporaryDirectory():
+    cwd = os.getcwd()
+    fsl_mat_fname = "fsl_style.mat"
+    fsl_mat = numpy.array(
+        [
+            [1.000000, 0.000000, -0.000935, 0.062539],
+            [0.000001, 0.999999, 0.001470, -0.162467],
+            [0.000935, -0.001470, 0.999999, -0.279038],
+            [0.000000, 0.000000, 0.000000, 1.000000]
+        ]
+    )
+    numpy.savetxt(fsl_mat_fname, fsl_mat, delimiter=' ')
+
+    in_filename = os.path.join(cwd, 'in_file.csv')
+    ants_mat = numpy.array([[
+        0, -0.99918075422702, 1.000000, 0.000000, -0.000935, 0.000001,
+        0.999999, 0.001470, 0.000935, -0.001470, 0.999999, -0.279038,
+        0.062539, -0.162467, -0.279038
+    ]])
+    numpy.savetxt(in_filename, ants_mat, delimiter=',', fmt='%.8f',
+                  header='this line is ignored')
+                  
+
+    # m2p - matrix 2 parameters
+    m2p = MotionCorr2FSLParams()
+    m2p.inputs.ants_matrix = in_filename
+    m2p.run()
+
+    pth, fname, _ = split_filename(in_filename)
+    conv_params_fname = '{}{}'.format(fname, '.par')
+    conv_params_fname = os.path.join(pth, conv_params_fname)
+
+    avscale = AvScale()
+    avscale.inputs.all_param = True
+    avscale.inputs.mat_file = fsl_mat_fname
+    avscale.run()
+    avscale_out = avscale.aggregate_outputs()
+    orig_params = []
+    orig_params.extend(avscale_out.rot_angles)
+    orig_params.extend(avscale_out.translations)
+    conv_params = numpy.genfromtxt(conv_params_fname, delimiter=' ')
+    comp = numpy.isclose(conv_params, orig_params)
+
+    assert(False not in comp)

From 77250b23ac0abd659feb29c893c10b88cdc8209f Mon Sep 17 00:00:00 2001
From: Ross Blair <rblair2@stanford.edu>
Date: Thu, 16 Mar 2017 17:02:32 -0700
Subject: [PATCH 45/48] add in c3d transformation - broken

---
 .../interfaces/ants/tests/test_MotionCorr2FSLParams.py | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
index ce24522c6f..87572ad6c7 100644
--- a/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
+++ b/nipype/interfaces/ants/tests/test_MotionCorr2FSLParams.py
@@ -2,6 +2,7 @@
 
 import numpy
 
+from nipype.interfaces.c3 import C3dAffineTool
 from nipype.interfaces.ants.preprocess import MotionCorr2FSLParams
 from nipype.interfaces.fsl.utils import AvScale
 from nipype.utils.tmpdirs import InTemporaryDirectory
@@ -21,6 +22,15 @@ def test_MotionCorr2FSLParams():
     )
     numpy.savetxt(fsl_mat_fname, fsl_mat, delimiter=' ')
 
+    c3 = C3dAffineTool()
+    c3.inputs.source_file = fsl_mat_fname
+    c3.inputs.itk_transform = 'affine.txt'
+    c3.inputs.fsl2ras = True
+    c3.run()
+    c3_out = c3.aggregate_outpus()
+
+    # ants = numpy.fromfile('affine.txt')
+
     in_filename = os.path.join(cwd, 'in_file.csv')
     ants_mat = numpy.array([[
         0, -0.99918075422702, 1.000000, 0.000000, -0.000935, 0.000001,

From d0d03b0c6cdef3807f79daf614f92f4c3fca4446 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 22 Mar 2017 11:46:33 -0700
Subject: [PATCH 46/48] use numpy to handle matrices

---
 nipype/interfaces/ants/preprocess.py | 47 ++++++++++++----------------
 1 file changed, 20 insertions(+), 27 deletions(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index 07c00e978d..d6dcab8428 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -6,7 +6,7 @@
 import os
 
 from nibabel.eulerangles import mat2euler
-import numpy
+import numpy as np
 
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
                     traits, isdefined, Str)
@@ -304,8 +304,9 @@ def _list_outputs(self):
             outputs['displacement_field'] = os.path.abspath(fname)
         return outputs
 
+
 class MotionCorr2FSLParamsInputSpec(BaseInterfaceInputSpec):
-    ants_matrix = File(
+    ants_moco = File(
         exists=True,
         desc='Motion correction matrices to be converted into FSL style motion parameters',
         mandatory=True
@@ -323,34 +324,26 @@ class MotionCorr2FSLParams(BaseInterface):
     input_spec = MotionCorr2FSLParamsInputSpec
     output_spec = MotionCorr2FSLParamsOutputSpec
 
+    def __init__(self, **inputs):
+        self._results = {}
+        super(MotionCorr2FSLParams, self).__init__(**inputs)
+
+    def _list_outputs(self):
+        return self._results
+
     def _run_interface(self, runtime):
-        in_fp = open(self.inputs.ants_matrix)
-        in_data = csv.reader(in_fp)
+        # Ants motion correction output has a single line header that we ignore
+        in_data = np.loadtxt(self.inputs.ants_moco,
+                             delimiter=',', skiprows=1, dtype=np.float32)[:, 2:]
         pars = []
+        for row in in_data:
+            mat = row[:9].reshape(3, 3)
+            param_z, param_y, param_x = mat2euler(mat)
+            pars.append([param_x, param_y, param_z] + row[9:].tolist())
 
-        # Ants motion correction output has a single line header that we ignore
-        next(in_data)
+        _, fname, _ = split_filename(self.inputs.ants_moco)
+        self._results['fsl_params'] = os.path.abspath('{}_fsl{}'.format(fname, '.par'))
+        np.savetxt(self._results['fsl_params'], pars, delimiter=' ')
 
-        for x in in_data:
-            mat = numpy.zeros((3, 3))
-            mat[0] = [x[2], x[3], x[4]]
-            mat[1] = [x[5], x[6], x[7]]
-            mat[2] = [x[8], x[9], x[10]]
-            param_z, param_y, param_x = mat2euler(mat)
-            pars.append([param_x, param_y, param_z, float(x[11]), float(x[12]),
-                        float(x[13])])
-
-        pth, fname, _ = split_filename(self.inputs.ants_matrix)
-        new_fname = '{}{}'.format(fname, '.par')
-        fsl_params_fname = os.path.join(pth, new_fname)
-        fsl_params = numpy.array(pars)
-        numpy.savetxt(fsl_params_fname, fsl_params, delimiter=' ')
         return runtime
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        pth, fname, _ = split_filename(self.inputs.ants_matrix)
-        new_fname = '{}{}'.format(fname, '.par')
-        out_file = os.path.join(pth, new_fname)
-        outputs["fsl_params"] = out_file
-        return outputs

From d8786aa2bf294669e0d9914741670bd480f4159a Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 22 Mar 2017 19:03:03 -0700
Subject: [PATCH 47/48] add moco2itk

---
 nipype/interfaces/ants/preprocess.py | 56 +++++++++++++++++++++++++++-
 1 file changed, 55 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index d6dcab8428..ef62966e65 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -5,8 +5,9 @@
 import csv
 import os
 
-from nibabel.eulerangles import mat2euler
 import numpy as np
+import nibabel as nb
+from nibabel.eulerangles import mat2euler
 
 from ..base import (BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File,
                     traits, isdefined, Str)
@@ -14,6 +15,14 @@
 from ...utils.filemanip import split_filename
 
 
+ITK_TFM_HEADER = "#Insight Transform File V1.0"
+ITK_TFM_TPL = """\
+#Transform {tf_id}
+Transform: {tf_type}
+Parameters: {tf_params}
+FixedParameters: {fixed_params}""".format
+
+
 class MotionCorrStatsInputSpec(ANTSCommandInputSpec):
     ''' Input spec for the antsMotionCorrStats command '''
     mask = File(argstr="-x %s", mandatory=True,
@@ -161,6 +170,7 @@ class MotionCorrOutputSpec(TraitedSpec):
     save_state = File(desc="The saved registration state to be restored")
     displacement_field = File(desc=("4D displacement field that captures the "
                                     "affine induced motion at each voxel"))
+    out_tfm = File(desc='write transforms in the Insight transform format')
 
 class MotionCorr(ANTSCommand):
     '''
@@ -212,6 +222,10 @@ class MotionCorr(ANTSCommand):
     input_spec = MotionCorrInputSpec
     output_spec = MotionCorrOutputSpec
 
+    def _run_interface(self, runtime):
+        runtime = super(MotionCorr, self)._run_interface(runtime)
+
+        return runtime
 
     def _gen_filename(self, name):
         '''
@@ -347,3 +361,43 @@ def _run_interface(self, runtime):
 
         return runtime
 
+def moco2itk(in_csv, in_reference, out_file=None):
+    """
+    Generates an Insight Transform File V1.0 from the motion correction
+    CSV file.
+
+    Would be replaced if finally `this issue <https://github.com/stnava/ANTs/issues/419>`_
+    is fixed.
+
+    """
+    from scipy.ndimage.measurements import center_of_mass
+
+    movpar = np.loadtxt(in_csv, dtype=float, skiprows=1,
+                        delimiter=',')[2:]
+
+    nii = nb.load(in_reference)
+
+    # Convert first to RAS, then to LPS
+    cmfixed = np.diag([-1, -1, 1, 1]).dot(nii.affine).dot(
+        list(center_of_mass(nii.get_data())) + [1])
+
+    tf_type = ('AffineTransform_double_3_3' if movpar.shape[1] == 12
+               else 'Euler3DTransform_double_3_3')
+
+    xfm_file = [ITK_TFM_HEADER]
+    for i, param in enumerate(movpar):
+        xfm_file.append(ITK_TFM_TPL(
+            tf_id=i, tf_type=tf_type,
+            tf_params=' '.join(['%.8f' % p for p in param]),
+            fixed_params=' '.join(['%.8f' % p for p in cmfixed[:3]])
+        ))
+    xfm_file += ['']
+
+    if out_file is None:
+        _, fname, _ = split_filename(in_reference)
+        out_file = os.path.abspath('{}_ants.tfm'.format(fname))
+
+    with open(out_file, 'w') as outfh:
+        outfh.write("\n".join(xfm_file))
+
+    return out_file

From e87346bbd4a12124c05b4d204779e7767da5fe9b Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 29 Apr 2017 18:29:57 -0700
Subject: [PATCH 48/48] add doctest, use name_source when possible

---
 nipype/interfaces/ants/preprocess.py | 100 ++++++++++++++-------------
 nipype/testing/data/ants_moco.csv    |   0
 2 files changed, 51 insertions(+), 49 deletions(-)
 create mode 100644 nipype/testing/data/ants_moco.csv

diff --git a/nipype/interfaces/ants/preprocess.py b/nipype/interfaces/ants/preprocess.py
index ef62966e65..c8c4943beb 100644
--- a/nipype/interfaces/ants/preprocess.py
+++ b/nipype/interfaces/ants/preprocess.py
@@ -31,7 +31,8 @@ class MotionCorrStatsInputSpec(ANTSCommandInputSpec):
         argstr="-m %s", mandatory=True,
         desc="motion correction parameter file to calculate statistics on"
     )
-    output = File(argstr="-o %s", hash_files=False, genfile=True,
+    output = File(name_source=['moco'], name_template='%s_fd.csv', keep_ext=False,
+                  argstr="-o %s", hash_files=False,
                   desc="csv file to output calculated statistics into")
     framewise = traits.Bool(argstr="-f %d",
                             desc="do framwise summarywise stats")
@@ -44,36 +45,43 @@ class MotionCorrStatsOutputSpec(TraitedSpec):
     output = File(desc="CSV file containg motion correction statistics", exists=True)
 
 class MotionCorrStats(ANTSCommand):
-    ''' Interface for the antsMotionCorrStats command '''
+    """
+    Interface for the antsMotionCorrStats command
+
+    Example
+    -------
+
+    >>> from nipype.interfaces.ants import MotionCorrStats
+    >>> stats = MotionCorrStats(framewise=True)
+    >>> stats.inputs.mask = 'brain_mask.nii'
+    >>> stats.inputs.moco = 'ants_moco.csv'
+    >>> stats.cmdline  # doctest: +ALLOW_UNICODE
+    'antsMotionCorrStats -f 1 -x brain_mask.nii -m ants_moco.csv -o ants_moco_fd.csv'
+
+    """
 
     _cmd = 'antsMotionCorrStats'
     input_spec = MotionCorrStatsInputSpec
     output_spec = MotionCorrStatsOutputSpec
 
-    def _gen_filename(self, name):
-        if name == 'output':
-            return "frame_displacement.csv"
-        return None
-
     def _list_outputs(self):
         outputs = self._outputs().get()
         if isdefined(self.inputs.output_spatial_map):
             outputs['spatial_map'] = (
                 os.path.abspath(self.inputs.output_spatial_map)
             )
-        if isdefined(self.inputs.output):
-            outputs['output'] = os.path.abspath(self.inputs.output)
         return outputs
 
 class MotionCorrInputSpec(ANTSCommandInputSpec):
     '''Input spec for the antsMotionCorr command.'''
-    dimension_desc = (
-        "This option forces the image to be treated as a "
-        "specified-dimensional image. If not specified, N4 tries to infer "
-        "the dimensionality from the input image."
-    )
-    dimensionality = traits.Enum(3, 2, argstr='-d %d', usedefault=True,
-                                 position=0, desc=dimension_desc)
+
+    dimensionality = traits.Enum(
+        3, 2, argstr='-d %d', usedefault=True, position=0,
+        desc=(
+            "This option forces the image to be treated as a "
+            "specified-dimensional image. If not specified, N4 tries to infer "
+            "the dimensionality from the input image."
+    ))
 
     average_image = File(argstr='-a %s', position=1, exists=False,
                          desc="4D image to take an average of.")
@@ -82,20 +90,18 @@ class MotionCorrInputSpec(ANTSCommandInputSpec):
                                        genfile=True, hash_files=False, argstr='%s')
 
     output_transform_prefix = Str(
-        desc="string to prepend to file containg the transformation parameters"
+        '', desc="string to prepend to file containg the transformation parameters"
     )
     output_warped_image = Str(desc="Name to save motion corrected image as.")
-
-    metric_type_desc = (
-        "GC : global correlation, CC: ANTS neighborhood cross correlation, "
-        "MI: Mutual information, and Demons: Thirion's Demons "
-        "(modified mean-squares). Note that the metricWeight is currently not "
-        "used. Rather, it is a temporary place holder until multivariate "
-        "metrics are available for a single stage."
-    )
-
-    metric_type = traits.Enum("CC", "MeanSquares", "Demons", "GC", "MI",
-                              "Mattes", argstr="%s", desc=metric_type_desc)
+    metric_type = traits.Enum(
+        "CC", "MeanSquares", "Demons", "GC", "MI", "Mattes", argstr="%s",
+        desc=(
+            "GC : global correlation, CC: ANTS neighborhood cross correlation, "
+            "MI: Mutual information, and Demons: Thirion's Demons "
+            "(modified mean-squares). Note that the metricWeight is currently not "
+            "used. Rather, it is a temporary place holder until multivariate "
+            "metrics are available for a single stage."
+    ))
     fixed_image = File(requires=['metric_type'],
                        desc="Fixed image to do motion correction with respect to.")
     moving_image = File(requires=['metric_type'],
@@ -158,6 +164,10 @@ class MotionCorrInputSpec(ANTSCommandInputSpec):
         desc="Write the low-dimensional 3D transforms to a 4D displacement field"
     )
 
+    out_composite_transform = File(
+        name_source=['output_transform_prefix'], name_template='%sMOCOparams.csv',
+        output_name='composite_transform', desc='output file containing head-motion transforms')
+
 
 
 class MotionCorrOutputSpec(TraitedSpec):
@@ -174,6 +184,12 @@ class MotionCorrOutputSpec(TraitedSpec):
 
 class MotionCorr(ANTSCommand):
     '''
+    Format and description of the affine motion correction parameters can be
+    found in this PDF starting on page 555 section 3.9.16 AffineTransform:
+    https://itk.org/ItkSoftwareGuide.pdf
+
+    https://github.com/stnava/ANTs/blob/master/Scripts/antsMotionCorrExample
+
     Examples
     -------
 
@@ -197,36 +213,27 @@ class MotionCorr(ANTSCommand):
     >>> ants_mc.inputs.gradient_step_length = 0.005
     >>> ants_mc.inputs.fixed_image = "average_image.nii.gz"
     >>> ants_mc.inputs.moving_image = "input.nii.gz"
-    >>> print(ants_mc.cmdline)
-    antsMotionCorr -d 3 -i 10x3 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1x1 -s 0.0x0.0 -t Affine[0.005] -u 1 -e 1
+    >>> ants_mc.cmdline  # doctest: +ALLOW_UNICODE
+    'antsMotionCorr -d 3 -i 10x3 -m GC[average_image.nii.gz,input.nii.gz,1.0,1,Random,0.05] -n\
+ 10 -o [motcorr,warped.nii.gz,average_image.nii.gz] -f 1x1 -s 0.0x0.0 -t Affine[0.005] -u 1 -e 1'
 
     >>> from nipype.interfaces.ants.preprocess import MotionCorr
     >>> ants_avg = MotionCorr()
     >>> ants_avg.inputs.average_image = 'input.nii.gz'
     >>> ants_avg.inputs.output_average_image = 'avg_out.nii.gz'
-    >>> print(ants_avg.cmdline)
-    antsMotionCorr -d 3 -a input.nii.gz -o avg_out.nii.gz
+    >>> ants_mc.cmdline  # doctest: +ALLOW_UNICODE
+    'antsMotionCorr -d 3 -a input.nii.gz -o avg_out.nii.gz'
 
     >>> ants_avg = MotionCorr()
     >>> ants_avg.inputs.average_image = 'input.nii.gz'
-    >>> print(ants_avg.cmdline)
-    antsMotionCorr -d 3 -a input.nii.gz -o input_avg.nii.gz
+    >>> ants_mc.cmdline  # doctest: +ALLOW_UNICODE
+    'antsMotionCorr -d 3 -a input.nii.gz -o input_avg.nii.gz'
 
-    Format and description of the affine motion correction parameters can be
-    found in this PDF starting on page 555 section 3.9.16 AffineTransform:
-    https://itk.org/ItkSoftwareGuide.pdf
-
-    https://github.com/stnava/ANTs/blob/master/Scripts/antsMotionCorrExample
     '''
     _cmd = 'antsMotionCorr'
     input_spec = MotionCorrInputSpec
     output_spec = MotionCorrOutputSpec
 
-    def _run_interface(self, runtime):
-        runtime = super(MotionCorr, self)._run_interface(runtime)
-
-        return runtime
-
     def _gen_filename(self, name):
         '''
         If a fixed image is specified we are not going to be outputting
@@ -306,11 +313,6 @@ def _list_outputs(self):
             outputs['warped_image'] = (
                 os.path.abspath(self.inputs.output_warped_image)
             )
-        if isdefined(self.inputs.output_transform_prefix):
-            fname = '{}MOCOparams.csv'.format(
-                self.inputs.output_transform_prefix
-            )
-            outputs['composite_transform'] = os.path.abspath(fname)
         if (isdefined(self.inputs.write_displacement) and
                 isdefined(self.inputs.output_transform_prefix) and
                 self.inputs.write_displacement is True):
diff --git a/nipype/testing/data/ants_moco.csv b/nipype/testing/data/ants_moco.csv
new file mode 100644
index 0000000000..e69de29bb2