MriImage-class {tractor.base}

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

xform

Numeric matrix giving the NIfTI-style xform matrix associated with the image, which indicates its orientation

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

find(fun = NULL, ..., array = TRUE)

Find voxels whose values are not zero, or satisfy a function

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

setData(newData)

Replace the data in the image

setOrigin(newOrigin)

Update the origin of the image

setSource(newSource)

Update the source of the image

setTags(..., merge = FALSE)

Add, replace or merge metadata tags

setXform(newXform)

Update the xform matrix associated with the image

summarise()

Summarise key aspects of the object

threshold(level, defaultValue = 0)

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