R: Creating MriImage objects from data

asMriImage {tractor.base}

R Documentation

Creating MriImage objects from data

Description

Functions for creating MriImage objects from data, including other images. All of these functions use data from arrays or MriImage objects to create a new MriImage object. asMriImage is the basic fucntion for creating an object from its constituents: an array of voxel values and some metadata (and/or a template image).

Usage

asMriImage(data, templateImage = nilObject(), imageDims = NA,
  voxelDims = NA, voxelDimUnits = NA, origin = NA, tags = NA,
  reordered = NA)

extractMriImage(image, dim, loc)

trimMriImage(image, clearance = 4, indices = NULL)

reorderMriImage(image)

Arguments

`data`	An array of pixel/voxel data.
`templateImage`	An optional `MriImage` object, to be used as a metadata template.
`imageDims`, `voxelDims`, `voxelDimUnits`, `origin`, `tags`, `reordered`	Metadata for the new image object. These values override any from the metadata object or data array. See `MriImage` class documentation for details.
`image`	An `MriImage` object.
`dim`, `loc`	The dimension and location along that dimension for which data should be extracted.
`clearance`	The number of voxels' clearance left around a trimmed image.
`indices`	A list of indices to keep along each dimension. Determined from the specified `clearance` if `NULL`.

Details

extractMriImage reduces the dimensionality of the source image by one, by extracting a single “slice” of data along one dimension. trimMriImage trims empty space from the edges of an image, reducing the dimensions of the image and thus avoiding the storage of lots of zeroes. reorderMriImage reorders the image data (and corresponding metadata) to the LAS convention, an operation which is usually performed when an image is read from file.

Value

An MriImage object.

Author(s)

Jon Clayden

References

Please cite the following reference when using TractoR in your work:

J.D. Clayden, S. Muñoz Maniega, A.J. Storkey, M.D. King, M.E. Bastin & C.A. Clark (2011). TractoR: Magnetic resonance imaging and tractography with R. Journal of Statistical Software 44(8):1-18. doi:10.18637/jss.v044.i08.