asNifti | R Documentation |
This function converts a filename, array or other image class into an object
of class "niftiImage"
, and optionally updates its metadata from a
reference image and/or changes its internal datatype. The dimensions and
pixel dimensions from the image
will replace those from the reference
object, if they are available.
asNifti(x, reference = NULL, ...)
## Default S3 method:
asNifti(x, reference = NULL, datatype = "auto",
internal = NA, ...)
x |
Any suitable object (see Details). |
reference |
An image, or a named list of NIfTI-1 properties like that
produced by |
... |
Additional parameters to methods. |
datatype |
The NIfTI datatype to use within the internal image. The
default, |
internal |
Logical value. If |
If the image
has an internal NIfTI pointer, that will be retrieved
directly. Otherwise, if it is a string, it will be taken to be a filename.
If it looks like a "nifti"
object (from package oro.nifti
),
or an "MriImage"
object (from package tractor.base
), a
conversion will be performed. A list will be assumed to be of the form
produced by niftiHeader
. Finally, a numeric array or matrix,
or RGB array, will be converted using default image parameters.
If reference
is a complete list of NIfTI-1 header fields, like that
produced by niftiHeader
, or an image, then it will be used to
create the internal object, and then the data and metadata associated with
the image
will overwrite the appropriate parts. If reference
is an incomplete list, the image
will be used to create the internal
object, and then the specified fields will be overwritten from the list.
This allows users to selectively update certain fields while leaving others
alone (but see the note below).
If multiple values are passed for a field that expects a scalar (which is most of them), the first element of the vector will be used, with a warning. An empty vector will be ignored, also with a warning. If a value of the wrong length is passed to a vector-valued field, an error will be generated.
Datatype information in a list reference
is ignored. The datatype can
only be changed using the datatype
argument, but in this case the
internal object gets out of sync with the R array, so an internal image is
returned to avoid the mismatch. Changing the internal datatype in this way
is for advanced usage only.
retrieveNifti
and updateNifti
are soft-deprecated alternative
interfaces to this function, which behave like the pre-existing functions of
the same names. They may be removed in future.
An array or internal image, with class "niftiImage"
(and
possibly also "internalImage"
).
The scl_slope
and scl_inter
fields affect the numerical
interpretation of the pixel data, so it is impossible in general to change
them without also changing the array values on both the C and the R side.
Therefore, to avoid unexpected side-effects, these fields are not affected
by this function. The dim
and pixdim
fields can be changed,
but for most users the accessor functions of the same name are much safer,
and should be used in preference.
Jon Clayden <code@clayden.org>
readNifti
, $.niftiImage
,
dim.internalImage
, pixdim
, xform
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