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DOC: add neuro / radio doc to tutorials
Fix up neuro / radio doc, I found it a bit confusing.
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doc/source/neuro_radio_conventions.rst

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@@ -28,17 +28,17 @@ are on the left or right of the subject and flip the images to the taste of
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the viewer. We could unpack these uses as *neurological display convention*
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and *radiological display convention*.
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**************************************
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Neurological / radiological voxel axes
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**************************************
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Radiological and neurological are sometimes used to refer to particular
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alignments of the voxel input axes to scanner RAS+ output axes. If we look at
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the affine mapping between voxel space and scanner RAS+, we may find that
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moving along the first voxel axis by one unit results in a equivalent scanner
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RAS+ movement that is mainly left to right. This can happen with a diagonal
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3x3 part of the affine mapping to scanner RAS+ (see
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:doc:`coordinate_systems`):
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*********************************
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Alignment of world and voxel axes
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*********************************
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As we will see in the next section, radiological and neurological are
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sometimes used to refer to particular alignments of the voxel input axes to
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scanner RAS+ output axes. If we look at the affine mapping between voxel space
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and scanner RAS+, we may find that moving along the first voxel axis by one
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unit results in a equivalent scanner RAS+ movement that is mainly left to
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right. This can happen with a diagonal 3x3 part of the affine mapping to
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scanner RAS+ (see :doc:`coordinate_systems`):
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.. plot::
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:context:
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Neurological / radiological voxel layout
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****************************************
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Very confusingly, some people also refer to images with "RAS" voxel axes as
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having "neurological" voxel layout. This is because the simplest way to
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display slices from this voxel array will result in the left of the subject
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appearing towards the left hand side of the screen and therefore neurological
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display convention. If we take a slice $k$ over the third axis of the image
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data array (``img_data[:, :, k]``), the resulting slice will have a first
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array axis going from left to right in terms of spatial position and the
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second array axis going from posterior to anterior. If we display this image
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with the first axis going from left to right on screen and the second from
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bottom to top, it will have the subject's right towards the right of the
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screen, and anterior towards the top of the screen, as neurologists like it.
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Here we are showing the middle slice of :download:`an image
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Very confusingly, some people refer to images with RAS voxel axes as having
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"neurological" voxel layout. This is because the simplest way to display
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slices from this voxel array will result in the left of the subject appearing
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towards the left hand side of the screen and therefore neurological display
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convention. If we take a slice $k$ over the third axis of the image data array
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(``img_data[:, :, k]``), the resulting slice will have a first array axis
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going from left to right in terms of spatial position and the second array
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axis going from posterior to anterior. If we display this image with the
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first axis going from left to right on screen and the second from bottom to
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top, it will have the subject's right towards the right of the screen, and
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anterior towards the top of the screen, as neurologists like it. Here we are
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showing the middle slice of :download:`an image
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</downloads/someones_anatomy.nii.gz>` with RAS voxel axes:
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.. plot::

doc/source/tutorials.rst

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@@ -7,4 +7,5 @@ General tutorials
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.. toctree::
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coordinate_systems
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neuro_radio_conventions
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dicom/dicom_intro

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