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Fix broken links in documentation (#1387)
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docs/source/README.rst

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@@ -22,7 +22,7 @@ or `k-space motion artifacts <http://proceedings.mlr.press/v102/shaw19a.html>`_.
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TorchIO is part of the official `PyTorch Ecosystem <https://pytorch.org/ecosystem/>`_,
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and was featured at
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the `PyTorch Ecosystem Day 2021 <https://pytorch.org/ecosystem/pted/2021>`_ and
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the `PyTorch Ecosystem Day 2021 <https://pytorch.org/blog/ecosystem_day_2021>`_ and
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the `PyTorch Developer Day 2021 <https://pytorch.org/blog/pytorch-developer-day-2021>`_.
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Many groups have used TorchIO for their research.

docs/source/quickstart.rst

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@@ -7,13 +7,8 @@ Installation
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The Python package is hosted on the
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`Python Package Index (PyPI) <https://pypi.org/project/torchio/>`_.
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To install the latest PyTorch version before installing TorchIO, it is
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recommended to use `light-the-torch <https://github.com/pmeier/light-the-torch>`_::
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$ pip install light-the-torch && ltt install torch
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The latest published version of TorchIO can be installed using Pip Installs
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Packages (``pip``)::
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Packages (PIP)::
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$ pip install torchio
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$ pip install torchio[plot]
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You can also install TorchIO with Conda::
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$ conda install -c conda-forge torchio
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If you are on Windows and have
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`trouble installing TorchIO <https://github.com/TorchIO-project/torchio/issues/343>`_,
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try `installing PyTorch <https://pytorch.org/get-started/locally/>`_ with
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`conda <https://docs.conda.io/en/latest/miniconda.html>`_ before pip-installing
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TorchIO.
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`conda <https://docs.conda.io/en/latest/miniconda.html>`_
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before pip-installing TorchIO.
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Hello, World!
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-------------
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t1=tio.ScalarImage('subject_a.nii.gz'),
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label=tio.LabelMap('subject_a.nii'),
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diagnosis='positive',
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age=36,
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)
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# Image files can be in any format supported by SimpleITK or NiBabel, including DICOM
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subject_b = tio.Subject(
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t1=tio.ScalarImage('subject_b_dicom_folder'),
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label=tio.LabelMap('subject_b_seg.nrrd'),
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diagnosis='negative',
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age=24,
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)
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# Images may also be created using PyTorch tensors or NumPy arrays
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t1=tio.ScalarImage(tensor=tensor_4d),
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label=tio.LabelMap(tensor=(tensor_4d > 0.5)),
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diagnosis='negative',
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age=19,
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)
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subjects_list = [subject_a, subject_b, subject_c]
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subjects_list = [
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subject_a,
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subject_b,
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subject_c,
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]
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# Let's use one preprocessing transform and one augmentation transform
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# This transform will be applied only to scalar images:

src/torchio/transforms/augmentation/intensity/random_spike.py

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@@ -14,7 +14,7 @@ class RandomSpike(RandomTransform, IntensityTransform, FourierTransform):
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r"""Add random MRI spike artifacts.
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Also known as `Herringbone artifact
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<https://radiopaedia.org/articles/herringbone-artifact?lang=gb>`_,
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<https://radiopaedia.org/articles/herringbone-artifact>`_,
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crisscross artifact or corduroy artifact, it creates stripes in different
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directions in image space due to spikes in k-space.
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