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Merged
merged 6 commits into from
Jul 3, 2018
Merged

DOCs: fix/improve descriptions for commands and interfaces #2593

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d0bc9c5
DOC: improve descriptions for N4BiasFieldCorrection InputSpec
yarikoptic May 22, 2018
10d3701
DOC: Unify short description of preprocess.FSLCommands
yarikoptic May 23, 2018
4a13087
DOC: Minor spelling fixes and further unification of short description
yarikoptic Jun 8, 2018
2a952f9
DOC: fix "joining spaces". Will stay with convention of leading space…
yarikoptic Jun 8, 2018
6a1e2e6
DOC: use wrapper in docstrings
mgxd Jul 3, 2018
c6c9093
Merge branch 'master' of https://github.com/nipy/nipype into doc-enhs…
mgxd Jul 3, 2018
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14 changes: 7 additions & 7 deletions nipype/interfaces/ants/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,8 +70,7 @@ class ANTSInputSpec(ANTSCommandInputSpec):
traits.Int(),
requires=['metric'],
mandatory=True,
desc='radius of the region (i.e. number of layers'
' around a voxel point)'
desc='radius of the region (i.e. number of layers around a voxel/pixel)'
' that is used for computing cross correlation')

output_transform_prefix = Str(
Expand Down Expand Up @@ -126,8 +125,8 @@ class ANTSOutputSpec(TraitedSpec):


class ANTS(ANTSCommand):
"""

"""ANTS wrapper for registration of images
(old, use Registration instead)

Examples
--------
Expand Down Expand Up @@ -557,7 +556,8 @@ class RegistrationOutputSpec(TraitedSpec):


class Registration(ANTSCommand):
"""
"""ANTs Registration command for registration of images

`antsRegistration <http://stnava.github.io/ANTs/>`_ registers a ``moving_image`` to a ``fixed_image``,
using a predefined (sequence of) cost function(s) and transformation operations.
The cost function is defined using one or more 'metrics', specifically
Expand Down Expand Up @@ -601,12 +601,12 @@ class Registration(ANTSCommand):
Examples
--------

Set up a Registation node with some default settings. This Node registers
Set up a Registration node with some default settings. This Node registers
'fixed1.nii' to 'moving1.nii' by first fitting a linear 'Affine' transformation, and
then a non-linear 'SyN' transformation, both using the Mutual Information-cost
metric.

The registration is initailized by first applying the (linear) transform
The registration is initialized by first applying the (linear) transform
trans.mat.

>>> import copy, pprint
Expand Down
18 changes: 9 additions & 9 deletions nipype/interfaces/ants/resampling.py
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Expand Up @@ -493,15 +493,15 @@ class ApplyTransformsToPointsInputSpec(ANTSCommandInputSpec):
argstr='--input %s',
mandatory=True,
desc=
("Currently, the only input supported is a csv file with "
"columns including x,y (2D), x,y,z (3D) or x,y,z,t,label (4D) column headers."
"The points should be defined in physical space."
"If in doubt how to convert coordinates from your files to the space"
"required by antsApplyTransformsToPoints try creating/drawing a simple"
"label volume with only one voxel set to 1 and all others set to 0."
"Write down the voxel coordinates. Then use ImageMaths LabelStats to find"
"out what coordinates for this voxel antsApplyTransformsToPoints is"
"expecting."),
("Currently, the only input supported is a csv file with"
" columns including x,y (2D), x,y,z (3D) or x,y,z,t,label (4D) column headers."
" The points should be defined in physical space."
" If in doubt how to convert coordinates from your files to the space"
" required by antsApplyTransformsToPoints try creating/drawing a simple"
" label volume with only one voxel set to 1 and all others set to 0."
" Write down the voxel coordinates. Then use ImageMaths LabelStats to find"
" out what coordinates for this voxel antsApplyTransformsToPoints is"
" expecting."),
exists=True)
output_file = traits.Str(
argstr='--output %s',
Expand Down
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