R: Create an image of a statistical peak.

mincRayTraceStats {RMINC}

R Documentation

Create an image of a statistical peak.

Description

Takes a voxel, an anatomical file, and a statistics file to create an image of the statistical peak.

Usage

mincRayTraceStats <- function(v, anatomy.volume, 
	statsbuffer, column=1, like.filename=NULL, mask=NULL,
	image.min=-1000, image.max=4000,
	output.width=800, output.height=800,
	place.inset=FALSE, inset=NULL,
	stats.largest.pos=NULL, stats.largest.neg=NULL,
	caption="t-statistic",
	fdr=NULL, slice.direction="transverse",
	outputfile="ray_trace_crosshair.png", 
	show.pos.and.neg=FALSE, display=TRUE)

Arguments

`v`	A mincVoxel indicating the voxel of interest.
`anatomy.volume`	The path to the file containing the anatomical data.
`statsbuffer`	Either the path to the stats file, a mincSingleDim, or a mincMultiDim.
`column`	If a mincMultiDim is specified, column will indicate which column of the data to use.
`like.filename`	If a column of a mincMultiDim is explicity passed through, a like file is needed to determine the dimensions of the stats buffer.
`mask`	If a mask is specified, the stats outside the mask will not be displayed in output image.
`image.min`	Specify the minimum image intensity.
`image.max`	Specify the maximum image intensity.
`output.width`	Specify the width of the output image.
`output.height`	Specify the height of the output image.
`place.inset`	Boolean indicating whether or not to place a 3D brain inset.
`inset`	Path to the object file (.obj) containing the surface of the brain.
`stats.largest.pos`	Specify the maximum stats value.
`stats.largest.neg`	Specify the minimum stats value.
`caption`	Specify the caption for the colourbar. If spaces occur in the caption use sometime along the line caption="\"Captoin with spaces\"".
`fdr`	Specify the statistical significance threshold.
`slice.direction`	The slice direction of the output image. This can be transverse, coronal or sagittal.
`outputfile`	The name (and path) of the outputfile.
`show.pos.and.neg`	In the case of t-statistics, when this flag is set to TRUE, the image will contain both the positive as well as the negative t-statistics.
`display`	Display the created image.

Details

This function will call the ray_trace program to create an image of a statistical peak. The anatomical slice of the brain will be overlayed with the statistical slice and a crosshair indicates the chosen peak.

Examples

## Not run: 
# read the text file describing the dataset
gf <- read.csv("control-file.csv")
# run a linear model relating the data in all voxels to Genotype
vs <- mincLm(filenames ~ Genotype, gf)
# get the voxel at world coordinates (1,0.5,-0.5)
v <- mincGetWorldVoxel(filenames, 1, 0.5, -0.5)
# create an image of this coordinate, using the third column
# of the mincLm output.
mincRayTraceStats(v,"/some/path/anatomical.mnc", vs[,3])
# or
mincRayTraceStats(v,"/some/path/anatomical.mnc", vs, column = 3)

## End(Not run)