diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index ec2cef1428f5c9cc2f816c9f9949a16041c15b9f..630116ec3252546a7eab17b2cf5d3c49b252a39b 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -456,7 +456,7 @@ class CoefficientField(NonLinearTransform):
:arg premat: If ``True``, the inverse :meth:`srcToRefMat` is applied
to the coordinates after the displacements have been
- addd.
+ added.
:returns: ``coords``, transformed into the source image space
"""
@@ -465,7 +465,7 @@ class CoefficientField(NonLinearTransform):
def displacements(self, coords):
- """Calculate the relative displacemenets for the given coordinates.
+ """Calculate the relative displacements for the given coordinates.
:arg coords: ``(N, 3)`` array of reference image voxel coordinates.
:return: A ``(N, 3)`` array of relative displacements to the
diff --git a/fsl/transform/x5.py b/fsl/transform/x5.py
index 3c784a8b6be29e37b741038183f2ffa81a1fdaa3..67f406628bc44b9b9ebc5e7100397375ff7b1bfd 100644
--- a/fsl/transform/x5.py
+++ b/fsl/transform/x5.py
@@ -88,18 +88,18 @@ shape, dimensions, and voxel-to-world affine transformation.
Groups of type *space* have the following fields:
-+-------------+-----------+---------------------------------------------------+
-| **Name** | **Type** | **Value/Description** |
-+-------------+-----------+---------------------------------------------------+
-| ``Type`` | attribute | ``'image'`` |
-+-------------+-----------+---------------------------------------------------+
-| ``Size`` | attribute | ``uint64`` ``(X, Y, Z)`` voxel dimensions |
-+-------------+-----------+---------------------------------------------------+
-| ``Scales`` | attribute | ``float64`` ``(X, Y, Z)`` voxel pixdims |
-+-------------+-----------+---------------------------------------------------+
-| ``Mapping`` | affine | The image voxel-to-world transformation (its |
-| | | ``sform``) |
-+-------------+-----------+---------------------------------------------------+
++--------------+-----------+--------------------------------------------------+
+| **Name** | **Type** | **Value/Description** |
++--------------+-----------+--------------------------------------------------+
+| ``Type`` | attribute | ``'image'`` |
++--------------+-----------+--------------------------------------------------+
+| ``Size`` | attribute | ``uint64`` ``(X, Y, Z)`` voxel dimensions |
++--------------+-----------+--------------------------------------------------+
+| ``Scales`` | attribute | ``float64`` ``(X, Y, Z)`` voxel pixdims |
++--------------+-----------+--------------------------------------------------+
+| ``Mapping/`` | affine | The image voxel-to-world transformation (its |
+| | | ``sform``) |
++--------------+-----------+--------------------------------------------------+
*deformation*
@@ -131,19 +131,19 @@ coordinate system.
Groups of type *deformation* have the following fields:
-+-------------+-----------+---------------------------------------------------+
-| **Name** | **Type** | **Value/Description** |
-+-------------+-----------+---------------------------------------------------+
-| ``Type`` | attribute | ``'deformation'`` |
-+-------------+-----------+---------------------------------------------------+
-| ``SubType`` | attribute | ``'absolute'`` or ``'relative'``. |
-+-------------+-----------+---------------------------------------------------+
-| ``Matrix`` | dataset | The deformation field - a ``float64`` array of |
-| | | shape ``(X, Y, Z, 3)`` |
-+-------------+-----------+---------------------------------------------------+
-| ``Mapping`` | affine | The field voxel-to-world transformation (its |
-| | | ``sform``) |
-+-------------+-----------+---------------------------------------------------+
++--------------+-----------+--------------------------------------------------+
+| **Name** | **Type** | **Value/Description** |
++--------------+-----------+--------------------------------------------------+
+| ``Type`` | attribute | ``'deformation'`` |
++--------------+-----------+--------------------------------------------------+
+| ``SubType`` | attribute | ``'absolute'`` or ``'relative'``. |
++--------------+-----------+--------------------------------------------------+
+| ``Matrix`` | dataset | The deformation field - a ``float64`` array of |
+| | | shape ``(X, Y, Z, 3)`` |
++--------------+-----------+--------------------------------------------------+
+| ``Mapping/`` | affine | The field voxel-to-world transformation (its |
+| | | ``sform``) |
++--------------+-----------+--------------------------------------------------+
Linear X5 files
@@ -204,7 +204,7 @@ between FLIRT-style matrices and X5 style matrices.
.. [*] For a given image, FSL coordinates are voxel coordinates scaled by the
- ``pixdim`` values in the NIFTI header, and an inversion along the X
+ ``pixdim`` values in the NIFTI header, with an inversion along the X
axis if the voxel-to-world affine (the ``sform``) has a positive
determinant.
@@ -269,9 +269,9 @@ Storage of FSL FNIRT warp fields in non-linear X5 files
-------------------------------------------------------
-FLIRT outputs the result of a non-linear registration from a source image to a
-reference image as either a warp field, or a coefficient field which can be
-used to generate a warp field. A warp field is defined in terms of the
+FLIRT outputs the result of a non-linear registration between a source image
+and a reference image as either a warp field, or a coefficient field which can
+be used to generate a warp field. A warp field is defined in terms of the
reference image - the warp field has the same shape and FOV as the reference
image, and contains either:
@@ -316,6 +316,7 @@ to source image world coordinates.
The :mod:`fsl.transform.fnirt` module contains functions which can be used to
perform all of the conversions and adjustments required to store FNIRT
transformations as X5 files.
+
"""
@@ -341,11 +342,11 @@ class X5Error(Exception):
def inferType(fname):
- """Return the type of the given X5 file - either ``'linear'``or
+ """Return the type of the given X5 file - either ``'linear'`` or
``'nonlinear'``.
:arg fname: Name of a X5 file
- :returns: ``'linear'``or ``'nonlinear'``
+ :returns: ``'linear'`` or ``'nonlinear'``
"""
with h5py.File(fname, 'r') as f:
@@ -405,7 +406,7 @@ def readNonLinearX5(fname):
"""Read a nonlinear X5 transformation file from ``fname``.
:arg fname: File name to read from
- :returns: A :class:`.DisplacementField` or :class:`.CoefficientField`
+ :returns: A :class:`.DeformationField`
"""
with h5py.File(fname, 'r') as f:
@@ -432,7 +433,7 @@ def writeNonLinearX5(fname, field):
"""Write a nonlinear X5 transformation to ``fname``.
:arg fname: File name to write to
- :arg field: A :class:`.DisplacementField` or :class:`.CoefficientField`
+ :arg field: A :class:`.DeformationField`
"""
with h5py.File(fname, 'w') as f:
diff --git a/fsl/wrappers/wrapperutils.py b/fsl/wrappers/wrapperutils.py
index 541c383a5a7d564ab37cde61cb47eff5c9a89fdd..c89afb2aadb002e1e6838235578ce124ce4caf41 100644
--- a/fsl/wrappers/wrapperutils.py
+++ b/fsl/wrappers/wrapperutils.py
@@ -448,7 +448,7 @@ class _FileOrThing(object):
``dict``-like object, where the function's actual return value is
accessible via an attribute called ``output``. All output arguments with a
value of ``LOAD`` will be present as dictionary entries, with the keyword
- argument names used as keys. Any ``LOAD``ed output arguments which were not
+ argument names used as keys. Any ``LOAD`` output arguments which were not
generated by the function will not be present in the dictionary.