R: The MriImage class

MriImage-class {tractor.base} | R Documentation

## The MriImage class

### Description

This class represents an MRI image. An object of this class is made up of some voxel data, stored as a sparse or dense numeric array, and some metadata, such as the file it was read from, the voxel dimensions, and so on. The group generic functions `Math`, `Ops` and `Summary` are defined for this class, as are methods for coercing to and from a standard `array`.

### Fields

`imageDims`

  Integer vector of dimensions

`voxelDims`

  Numeric vector of pixel/voxel spacings

`voxelDimUnits`

  Character vector of spatial and/or temporal spacing units. Millimetres and seconds (i.e., c("mm","s")) are typical

`source`

  String naming the file(s) that the image was read from. This is reset to the empty string if the image is modified

`origin`

  Numeric vector giving the spatial coordinate origin

`storedXform`

  Numeric matrix giving the NIfTI xform matrix read from file, if any

`reordered`

  Logical value indicating whether the image has been reordered. See `reorderMriImage`

`tags`

  Named list of arbitrary DICOM-style tags

`data`

  Sparse or dense array of data, or `NULL`

### Methods

`apply(...)`

  Apply a function to the margins of the image

`binarise()`

  Binarise the image by setting nonzero values to one

`fill(value)`

  Fill the image with a particular value

`getDataAtPoint(...)`

  Obtain the value of the image at a particular point

`getMetadata()`

  Obtain a version of the image with any data removed

`getNonzeroIndices(array = TRUE, positiveOnly = FALSE)`

  Find voxels whose values are not zero

`getSlice(dim, loc)`

  Extract data from a slice of the image along one dimension

`getSparseness()`

  Obtain the proportion of zeroes in the image

`getTags(keys = NULL)`

  Retrieve some or all of the tags stored with the image

`getXform(implicit = TRUE)`

  Retrieve the stored or implicit xform matrix

`map(fun, ..., sparse = NULL)`

  Replace the current data with the result of a function

`mask(maskImage)`

  Mask the image, setting zero voxels in the mask to zero

`setOrigin(newOrigin)`

  Update the origin of the image

`setSource(newSource)`

  Update the source of the image

`setXform(newXform)`

  Update the xform matrix associated with the image

`threshold(level, defaultValue = 0)`

  Threshold the image by setting values below the threshold level to zero

[Package tractor.base version 3.2.2 Index]