@@ -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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-
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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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+
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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:
@@ -66,18 +66,18 @@ Some people therefore refer to this alignment of voxel and RAS+ axes as
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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 ::
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