R: Visualise MriImage objects

createSliceGraphic {tractor.base}

R Documentation

Visualise MriImage objects

Description

Visualise MriImage objects noninteractively using an R graphics device. See viewImages for an interactive alternative. These functions create 2D visualisations of 3D images by slicing or maximum intensity projection.

Usage

createSliceGraphic(image, x = NA, y = NA, z = NA,
  device = c("internal", "png"), colourScale = 1, add = FALSE,
  file = NULL, zoomFactor = 1, windowLimits = NULL)

createProjectionGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL)

createContactSheetGraphic(image, axis, device = c("internal", "png"),
  colourScale = 1, add = FALSE, file = NULL, zoomFactor = 1,
  windowLimits = NULL, clearance = NULL, nColumns = NULL)

Arguments

`image`	An `MriImage` object.
`x`, `y`, `z`	Integer vectors, each of length 1. Exactly one of these must be specified to indicate the plane of interest.
`device`	Either `"internal"` for display on the default graphics device, or `"png"` for creating PNG format image file(s). Abbreviations are fine.
`colourScale`	A colour scale definition, of the sort generated by `getColourScale`.
`add`	Overlay the graphic on a previous one. Used only when `device` is `"internal"`.
`file`	A file name, to be used when `device` is `"png"`.
`zoomFactor`	Factor by which to enlarge the image. Applies only when `device` is `"png"`.
`windowLimits`	Numeric vector of length 2 giving the limits of the colour scale, or `NULL` for limits matching the range of the image data. Passed as the `zlim` argument to `image`.
`axis`	A vector of axes along which slice/projection images should be created. 1 is left-right, 2 is anterior-posterior, 3 is superior-inferior.
`clearance`	Number of voxels' clearance to leave around each slice image in the contact sheet. Passed to `trimMriImage`.
`nColumns`	Number of slices per row in the contact sheet grid. If `NULL`, the function will aim for a square grid.

Value

These functions are called for their side effects.

Note

When the device option is set to "png", the "png" and "mmand" packages are required by these functions.

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.