@@ -281,6 +281,41 @@ the sform: ``get_qform()``, ``set_qform()``.
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The qform also has a corresponding ``qform_code `` with the same interpretation
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as the `sform_code `.
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+ The fall-back header affine
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+ ===========================
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+
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+ This is the affine of last resort, constructed only from the ``pixdim `` voxel
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+ sizes. The `NIfTI specification <nifti1 >`_ says that this should set the
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+ first voxel in the image as [0, 0, 0] in world coordinates, but we nibabblers
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+ follow SPM _ in preferring to set the central voxel to have [0, 0, 0] world
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+ coordinate. The NIfTI spec also implies that the image should be assumed to be
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+ in RAS+ *voxel * orientation for this affine (see :doc: `coordinate_systems `).
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+ Again like SPM, we prefer to assume LAS+ voxel orientation by default.
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+
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+ You can always get the fall-back affine with ``get_base_affine() ``:
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+
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+ >>> n1_header.get_base_affine()
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+ array([[ -2. , 0. , 0. , 127. ],
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+ [ 0. , 2. , 0. , -95. ],
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+ [ 0. , 0. , 2.2, -25.3],
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+ [ 0. , 0. , 0. , 1. ]])
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+
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+ .. _choosing-image-affine :
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+
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+ Choosing the image affine
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+ =========================
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+
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+ Given there are three possible affines defined in the NIfTI header, nibabel
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+ has to chose which of these to use for the image ``affine ``.
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+
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+ The algorithm is defined in the ``get_best_affine() `` method. It is:
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+
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+ #. If ``sform_code `` != 0 ('unknown') use the sform affine; else
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+ #. If ``qform_code `` != 0 ('unknown') use the qform affine; else
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+ #. Use the fall-back affine.
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+
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+ .. _default-sform-qform-codes :
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+
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Default sform and qform codes
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=============================
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@@ -336,39 +371,6 @@ If you wish to set the sform and qform affines and/or codes to some other
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value, you can always set them after creation using the ``set_sform `` and
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``set_qform `` methods, as described above.
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- The fall-back header affine
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- ===========================
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-
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- This is the affine of last resort, constructed only from the ``pixdim `` voxel
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- sizes. The `NIfTI specification <nifti1 >`_ says that this should set the
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- first voxel in the image as [0, 0, 0] in world coordinates, but we nibabblers
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- follow SPM _ in preferring to set the central voxel to have [0, 0, 0] world
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- coordinate. The NIfTI spec also implies that the image should be assumed to be
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- in RAS+ *voxel * orientation for this affine (see :doc: `coordinate_systems `).
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- Again like SPM, we prefer to assume LAS+ voxel orientation by default.
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-
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- You can always get the fall-back affine with ``get_base_affine() ``:
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-
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- >>> n1_header.get_base_affine()
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- array([[ -2. , 0. , 0. , 127. ],
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- [ 0. , 2. , 0. , -95. ],
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- [ 0. , 0. , 2.2, -25.3],
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- [ 0. , 0. , 0. , 1. ]])
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-
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- .. _choosing-image-affine :
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-
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- Choosing the image affine
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- =========================
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-
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- Given there are three possible affines defined in the NIfTI header, nibabel
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- has to chose which of these to use for the image ``affine ``.
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-
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- The algorithm is defined in the ``get_best_affine() `` method. It is:
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-
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- #. If ``sform_code `` != 0 ('unknown') use the sform affine; else
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- #. If ``qform_code `` != 0 ('unknown') use the qform affine; else
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- #. Use the fall-back affine.
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-
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************
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Data scaling
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************
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