@@ -19,4 +19,3 @@ and `UL1 TR000442	University of Iowa Clinical and Translational Science Program
 
 
 We would also like to thank `JetBrains <http://www.jetbrains.com/>`__ for providing `Pycharm <http://www.jetbrains.com/pycharm/>`__ licenses.
-

@@ -11,4 +11,4 @@ <h3>{{ _('Links') }}</h3>
 <a href='https://pypi.python.org/pypi/nipype/'><img src='https://img.shields.io/pypi/pyversions/nipype.svg' alt='Python Versions' /></a></li>
 </ul>
 
-{% endblock %}
+{% endblock %}

@@ -13,4 +13,3 @@
 <a class="navbar" href="{{pathto('developers')}}">Developers</a> ·
 <a class="navbar" href="{{pathto('about')}}">About</a> ·
 <a class="navbar" href="http://nipy.org">Nipy</a>
-

@@ -169,4 +169,3 @@ absolute path is generated and used for the ``cmdline`` when run, but
 
 In [80]: res.interface.inputs.outfile
 Out[80]: 'bar.nii'
-

@@ -30,4 +30,3 @@ Create your own forked copy of nipype_
 should find yourself at the home page for your own forked copy of nipype_.
 
 .. include:: links.inc
-

@@ -13,4 +13,3 @@ Contents:
 set_up_fork
 configure_git
 development_workflow
-

@@ -14,5 +14,3 @@ Contents:
 ing
 git_development
 git_resources
-
-

@@ -65,4 +65,3 @@ Just for your own satisfaction, show yourself that you now have a new
 origin	[email protected]:your-user-name/nipype.git (push)
 
 .. include:: links.inc
-

@@ -287,7 +287,7 @@ def clear_runs_since(self, day=None, month=None, year=None, warn=True):
 os.remove(log_name)
 
 def _clear_all_but(self, runs, warn=True):
-"""Remove all the runs appart from those given to the function
+"""Remove all the runs apart from those given to the function
 input.
 """
 rm_all_but(self.base_dir, set(runs.keys()), warn=warn)

@@ -262,8 +262,8 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True, ext=None)
 Generate a filename based on the given parameters.
 
 The filename will take the form: cwd/basename<suffix><ext>.
-If change_ext is True, it will use the extentions specified in
-<instance>intputs.output_type.
+If change_ext is True, it will use the extensions specified in
+<instance>inputs.output_type.
 
 Parameters
 ----------

@@ -265,7 +265,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
 class DeconvolveOutputSpec(TraitedSpec):
 out_file = File(desc="output statistics file", exists=True)
 reml_script = File(
-desc="automatical generated script to run 3dREMLfit", exists=True
+desc="automatically generated script to run 3dREMLfit", exists=True
 )
 x1D = File(desc="save out X matrix", exists=True)
 cbucket = File(desc="output regression coefficients file (if generated)")
@@ -528,7 +528,7 @@ class RemlfitInputSpec(AFNICommandInputSpec):
 "be included.",
 argstr="-Rglt %s",
 )
-fitts_file = File(desc="ouput dataset for REML fitted model", argstr="-Rfitts %s")
+fitts_file = File(desc="output dataset for REML fitted model", argstr="-Rfitts %s")
 errts_file = File(
 desc="output dataset for REML residuals = data - fitted model",
 argstr="-Rerrts %s",
@@ -584,7 +584,7 @@ class RemlfitOutputSpec(AFNICommandOutputSpec):
 "but ONLY for the GLTs added on the REMLfit command "
 "line itself via 'gltsym' (if generated)"
 )
-fitts_file = File(desc="ouput dataset for REML fitted model (if generated)")
+fitts_file = File(desc="output dataset for REML fitted model (if generated)")
 errts_file = File(
 desc="output dataset for REML residuals = data - fitted model (if " "generated"
 )

@@ -821,7 +821,7 @@ class AutoTLRCInputSpec(CommandLineInputSpec):
 
 
 class AutoTLRC(AFNICommand):
-"""A minmal wrapper for the AutoTLRC script
+"""A minimal wrapper for the AutoTLRC script
 The only option currently supported is no_ss.
 For complete details, see the `3dQwarp Documentation.
 <https://afni.nimh.nih.gov/pub/dist/doc/program_help/@auto_tlrc.html>`_
@@ -1327,7 +1327,7 @@ class ECMInputSpec(CentralityInputSpec):
 )
 fecm = traits.Bool(
 desc="Fast centrality method; substantial speed increase but cannot "
-"accomodate thresholding; automatically selected if -thresh or "
+"accommodate thresholding; automatically selected if -thresh or "
 "-sparsity are not set",
 argstr="-fecm",
 )
@@ -2933,7 +2933,7 @@ class TProjectInputSpec(AFNICommandInputSpec):
 the output dataset:
 
 * mode = ZERO -- put zero values in their place;
-output datset is same length as input
+output dataset is same length as input
 * mode = KILL -- remove those time points;
 output dataset is shorter than input
 * mode = NTRP -- censored values are replaced by interpolated
@@ -3073,7 +3073,7 @@ class TProject(AFNICommand):
 as ``-passband``. In this way, you can bandpass time-censored data, and at
 the same time, remove other time series of no interest
 (e.g., physiological estimates, motion parameters).
-Shifts voxel time series from input so that seperate slices are aligned to
+Shifts voxel time series from input so that separate slices are aligned to
 the same temporal origin.
 
 Examples
@@ -3188,7 +3188,7 @@ class TShiftOutputSpec(AFNICommandOutputSpec):
 
 
 class TShift(AFNICommand):
-"""Shifts voxel time series from input so that seperate slices are aligned
+"""Shifts voxel time series from input so that separate slices are aligned
 to the same temporal origin.
 
 For complete details, see the `3dTshift Documentation.
@@ -3658,7 +3658,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
 with 3dNwarpApply and 3dNwarpCat, for example.
 * To be clear, this is the warp from source dataset
 coordinates to base dataset coordinates, where the
-values at each base grid point are the xyz displacments
+values at each base grid point are the xyz displacements
 needed to move that grid point's xyz values to the
 corresponding xyz values in the source dataset:
 base( (x,y,z) + WARP(x,y,z) ) matches source(x,y,z)
@@ -4034,7 +4034,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
 The goal is greater speed, and it seems to help this"
 positively piggish program to be more expeditious."
 * However, accuracy is somewhat lower with '-duplo',"
-for reasons that currenly elude Zhark; for this reason,"
+for reasons that currently elude Zhark; for this reason,"
 the Emperor does not usually use '-duplo'.
 
 """,
@@ -4225,21 +4225,21 @@ class QwarpInputSpec(AFNICommandInputSpec):
 )
 hel = traits.Bool(
 desc="Hellinger distance: a matching function for the adventurous"
-"This option has NOT be extensively tested for usefullness"
+"This option has NOT be extensively tested for usefulness"
 "and should be considered experimental at this infundibulum.",
 argstr="-hel",
 xor=["nmi", "mi", "lpc", "lpa", "pear"],
 )
 mi = traits.Bool(
 desc="Mutual Information: a matching function for the adventurous"
-"This option has NOT be extensively tested for usefullness"
+"This option has NOT be extensively tested for usefulness"
 "and should be considered experimental at this infundibulum.",
 argstr="-mi",
 xor=["mi", "hel", "lpc", "lpa", "pear"],
 )
 nmi = traits.Bool(
 desc="Normalized Mutual Information: a matching function for the adventurous"
-"This option has NOT been extensively tested for usefullness"
+"This option has NOT been extensively tested for usefulness"
 "and should be considered experimental at this infundibulum.",
 argstr="-nmi",
 xor=["nmi", "hel", "lpc", "lpa", "pear"],

@@ -539,27 +539,27 @@ class CatInputSpec(AFNICommandInputSpec):
 argstr="-sel %s",
 )
 out_int = traits.Bool(
-desc="specifiy int data type for output",
+desc="specify int data type for output",
 argstr="-i",
 xor=["out_format", "out_nice", "out_double", "out_fint", "out_cint"],
 )
 out_nice = traits.Bool(
-desc="specifiy nice data type for output",
+desc="specify nice data type for output",
 argstr="-n",
 xor=["out_format", "out_int", "out_double", "out_fint", "out_cint"],
 )
 out_double = traits.Bool(
-desc="specifiy double data type for output",
+desc="specify double data type for output",
 argstr="-d",
 xor=["out_format", "out_nice", "out_int", "out_fint", "out_cint"],
 )
 out_fint = traits.Bool(
-desc="specifiy int, rounded down, data type for output",
+desc="specify int, rounded down, data type for output",
 argstr="-f",
 xor=["out_format", "out_nice", "out_double", "out_int", "out_cint"],
 )
 out_cint = traits.Bool(
-desc="specifiy int, rounded up, data type for output",
+desc="specify int, rounded up, data type for output",
 xor=["out_format", "out_nice", "out_double", "out_fint", "out_int"],
 )
 
@@ -693,7 +693,7 @@ class CenterMassInputSpec(CommandLineInputSpec):
 argstr="-set %f %f %f",
 )
 local_ijk = traits.Bool(
-desc="Output values as (i,j,k) in local orienation", argstr="-local_ijk"
+desc="Output values as (i,j,k) in local orientation", argstr="-local_ijk"
 )
 roi_vals = traits.List(
 traits.Int,
@@ -2554,11 +2554,11 @@ class ReHoInputSpec(CommandLineInputSpec):
 
 class ReHoOutputSpec(TraitedSpec):
 out_file = File(exists=True, desc="Voxelwise regional homogeneity map")
-out_vals = File(desc="Table of labelwise regional homogenity values")
+out_vals = File(desc="Table of labelwise regional homogeneity values")
 
 
 class ReHo(AFNICommandBase):
-"""Compute regional homogenity for a given neigurhood.l,
+"""Compute regional homogeneity for a given neigurhood.l,
 based on a local neigrhood of that voxel.
 
 For complete details, see the `3dReHo Documentation.
@@ -2740,7 +2740,7 @@ class TCatSBInputSpec(AFNICommandInputSpec):
 
 class TCatSubBrick(AFNICommand):
 """Hopefully a temporary function to allow sub-brick selection until
-afni file managment is improved.
+afni file management is improved.
 
 For complete details, see the `3dTcat Documentation.
 <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcat.html>`_

@@ -84,7 +84,7 @@ class C3dInputSpec(CommandLineInputSpec):
 desc=(
 "Write all images on the convert3d stack as multiple files."
 " Supports both list of output files or a pattern for the output"
-" filenames (using %d substituion)."
+" filenames (using %d substitution)."
 ),
 )
 pix_type = traits.Enum(

@@ -55,7 +55,7 @@ class NiftiGeneratorBase(BaseInterface):
 embedded meta data."""
 
 def _get_out_path(self, meta, idx=None):
-"""Return the output path for the gernerated Nifti."""
+"""Return the output path for the generated Nifti."""
 if self.inputs.out_format:
 out_fmt = self.inputs.out_format
 else:
@@ -262,7 +262,7 @@ def _outputs(self):
 return outputs
 
 def _run_interface(self, runtime):
-# If the 'meta_keys' input is a list, covert it to a dict
+# If the 'meta_keys' input is a list, convert it to a dict
 self._make_name_map()
 nw = NiftiWrapper.from_filename(self.inputs.in_file)
 self.result = {}
@@ -342,7 +342,7 @@ class MergeNiftiInputSpec(NiftiGeneratorBaseInputSpec):
 merge_dim = traits.Int(
 desc="Dimension to merge along. If not "
 "specified, the last singular or "
-"non-existant dimension is used."
+"non-existent dimension is used."
 )
 
 

@@ -2361,8 +2361,8 @@ def _format_arg(self, name, spec, value):
 def _list_outputs(self):
 outputs = self.output_spec().get()
 cwd = os.getcwd()
-prefices = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
-suffices = dict(
+prefixes = dict(src=self.inputs.source_file, trg=self.inputs.target_file)
+suffixes = dict(
 out_reg_file=("src", "_robustreg.lta", False),
 registered_file=("src", "_robustreg", True),
 weights_file=("src", "_robustweights", True),
@@ -2372,12 +2372,12 @@ def _list_outputs(self):
 half_source_xfm=("src", "_robustxfm.lta", False),
 half_targ_xfm=("trg", "_robustxfm.lta", False),
 )
-for name, sufftup in list(suffices.items()):
+for name, sufftup in list(suffixes.items()):
 value = getattr(self.inputs, name)
 if value:
 if value is True:
 outputs[name] = fname_presuffix(
-prefices[sufftup[0]],
+prefixes[sufftup[0]],
 suffix=sufftup[1],
 newpath=cwd,
 use_ext=sufftup[2],

@@ -764,7 +764,7 @@ def _list_outputs(self):
 out_files.append(s3dst)
 # Otherwise, copy locally src -> dst
 if not s3_flag or isdefined(self.inputs.local_copy):
-# Create output directory if it doesnt exist
+# Create output directory if it doesn't exist
 if not os.path.exists(path):
 try:
 os.makedirs(path)
@@ -1318,7 +1318,7 @@ class SelectFilesInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
 sort_filelist = traits.Bool(
 True,
 usedefault=True,
-desc="When matching mutliple files, return them" " in sorted order.",
+desc="When matching multiple files, return them" " in sorted order.",
 )
 raise_on_empty = traits.Bool(
 True,
@@ -1346,7 +1346,7 @@ class SelectFiles(IOBase):
 
 This interface uses Python's {}-based string formatting syntax to plug
 values (possibly known only at workflow execution time) into string
-templates and collect files from persistant storage. These templates can
+templates and collect files from persistent storage. These templates can
 also be combined with glob wildcards (``*``, ``?``) and character ranges (``[...]``).
 The field names in the formatting template (i.e. the terms in braces) will
 become inputs fields on the interface, and the keys in the templates
@@ -1513,7 +1513,7 @@ class DataFinder(IOBase):
 Will recursively search any subdirectories by default. This can be limited
 with the min/max depth options.
 Matched paths are available in the output 'out_paths'. Any named groups of
-captured text from the regular expression are also available as ouputs of
+captured text from the regular expression are also available as outputs of
 the same name.
 
 Examples
@@ -1583,7 +1583,7 @@ def _run_interface(self, runtime):
 ]
 self.result = None
 for root_path in self.inputs.root_paths:
-# Handle tilda/env variables and remove extra seperators
+# Handle tilda/env variables and remove extra separators
 root_path = os.path.normpath(
 os.path.expandvars(os.path.expanduser(root_path))
 )
@@ -1612,7 +1612,7 @@ def _run_interface(self, runtime):
 for key, vals in list(self.result.items()):
 self.result[key] = vals[0]
 else:
-# sort all keys acording to out_paths
+# sort all keys according to out_paths
 for key in list(self.result.keys()):
 if key == "out_paths":
 continue
@@ -2083,15 +2083,15 @@ class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec):
 
 assessor_id = Str(
 desc=(
-"Option to customize ouputs representation in XNAT - "
+"Option to customize outputs representation in XNAT - "
 "assessor level will be used with specified id"
 ),
 xor=["reconstruction_id"],
 )
 
 reconstruction_id = Str(
 desc=(
-"Option to customize ouputs representation in XNAT - "
+"Option to customize outputs representation in XNAT - "
 "reconstruction level will be used with specified id"
 ),
 xor=["assessor_id"],

@@ -191,7 +191,7 @@ def _gen_matlab_command(self, argstr, script_lines):
 else:
 prescript.insert(0, "fprintf(1,'Executing code at %s:\\n',datestr(now));")
 for path in paths:
-# addpath() is not available after compliation
+# addpath() is not available after compilation
 # https://www.mathworks.com/help/compiler/ismcc.html
 # https://www.mathworks.com/help/compiler/isdeployed.html
 prescript.append("if ~(ismcc || isdeployed), addpath('%s'); end;\n" % path)