diff --git a/fsl/data/dicom.py b/fsl/data/dicom.py index 756e1ccb1c826ddb96dcf806a6169b9d17b0b9c1..57e0a227da55527e36f3166a81379ee57fd9b72e 100644 --- a/fsl/data/dicom.py +++ b/fsl/data/dicom.py @@ -18,10 +18,10 @@ wrappers around functionality provided by Chris Rorden's ``dcm2niix`` program: scanDir loadSeries +See: https://github.com/rordenlab/dcm2niix/ + .. note:: These functions will not work if an executable called ``dcm2niix`` cannot be found. - -.. see:: https://github.com/rordenlab/dcm2niix/ """ diff --git a/fsl/data/mesh.py b/fsl/data/mesh.py index 829a911e3ea6a15c44f801519ea9eec65dcbeb8c..59fc266c702e3b82427be74fc764ab41d0797c70 100644 --- a/fsl/data/mesh.py +++ b/fsl/data/mesh.py @@ -129,7 +129,7 @@ class Mesh(notifier.Notifier, meta.Meta): selected vertex set. - **Metadata* + **Metadata** The ``Mesh`` class also inherits from the :class:`Meta` class, so @@ -625,13 +625,14 @@ class Mesh(notifier.Notifier, meta.Meta): triangle vertices. :returns: A tuple containing + - A ``(m, 2, 3)`` array containing ``m`` vertices: of a set of lines, defining the plane intersection - A ``(m,)`` array containing the indices of the ``m`` triangles that were intersected. - - (if ``distances is True``) A ``(m, 2, 3)`` arra + - (if ``distances is True``) A ``(m, 2, 3)`` array containing the barycentric coordinates of each line vertex with respect to its intersected triangle. diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py index 485b687e336f7fef49cf831eb390072df6e96b6e..6c36340d923c8df61ddc8a5ee0ca2d308bde54dc 100644 --- a/fsl/data/mghimage.py +++ b/fsl/data/mghimage.py @@ -32,9 +32,9 @@ class MGHImage(fslimage.Image): """The ``MGHImage`` class is a NIFTI :class:`Image` which has been converted from a Freesurfer ``.mgh`` file. - .. see:: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat - - .. see:: http://nipy.org/nibabel/reference/nibabel.freesurfer.html + See: + - https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat + - http://nipy.org/nibabel/reference/nibabel.freesurfer.html """ def __init__(self, image, *args, **kwargs): diff --git a/fsl/data/vtk.py b/fsl/data/vtk.py index f39a868ef16d68137cc829769856ecf2be27e954..62ee14111692b7cc5939a0e1da898c3b3e183671 100644 --- a/fsl/data/vtk.py +++ b/fsl/data/vtk.py @@ -12,7 +12,7 @@ A handful of convenience functions are also in this module: .. autosummary:: :nosignatures: - loadVTKPolyDataFile + loadVTKPolydataFile getFIRSTPrefix findReferenceImage diff --git a/fsl/utils/tempdir.py b/fsl/utils/tempdir.py index 9896c91584f0b0abf1d4d3080a7e11e39f0d2dae..b819058f804d22a225fc37f5ba15eb5418c55de8 100644 --- a/fsl/utils/tempdir.py +++ b/fsl/utils/tempdir.py @@ -8,7 +8,7 @@ directories. It currently only contains one function: .. autosummary:: - :nosignature: + :nosignatures: tempdir """ diff --git a/fsl/wrappers/melodic.py b/fsl/wrappers/melodic.py index e5ceb738b14d4c1533d8c2a018434b07037a5655..b95aeabfa9c4ee287d18fbf3fa76f7d4fa90297d 100644 --- a/fsl/wrappers/melodic.py +++ b/fsl/wrappers/melodic.py @@ -5,8 +5,8 @@ # Author: Sean Fitzgibbon <sean.fitzgibbon@ndcn.ox.ac.uk> # Author: Paul McCarthy <pauldmccarthy@gmail.com> # -"""This module provides wrapper functions for the FSL `MELODIC -<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other +"""This module provides wrapper functions for the FSL +`MELODIC <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC>`_ tool, and other related utilities. .. autosummary:: @@ -25,7 +25,7 @@ from . import wrapperutils as wutils @wutils.fileOrImage('input', 'mask', 'ICs', 'bgimage') @wutils.fslwrapper def melodic(input, **kwargs): - """Multivariate Exploratory Linear Optimised ICA.""" + """Wrapper for the ``melodic`` command.""" valmap = { 'Oall' : wutils.SHOW_IF_TRUE, @@ -62,7 +62,7 @@ def melodic(input, **kwargs): @wutils.fileOrArray('design', 'out_mix') @wutils.fslwrapper def fsl_regfilt(input, out, design, **kwargs): - """Wrapper for the ``fsl_regfilt``command. """ + """Wrapper for the ``fsl_regfilt`` command. """ asrt.assertIsNifti(input, out)