mincRayTraceStats: Create an image of a statistical peak.

In Mouse-Imaging-Centre/RMINC: Statistical Tools for Medical Imaging NetCDF (MINC) Files

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(
  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,
  clobber = NULL,
  tmpdir = "/tmp"
)

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.
clobber	Overwrite existing output file when set to TRUE, will not overwrite when set to FALSE and will prompt when NULL.
tmpdir	Specify a directory for temporary files.

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.

See Also

mincLm, mincFDR, mincMean, mincSd

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], like.filename = "like-this-file.mnc")
# in this particular case, a like file is stored with the vs object and
# can be retrieved using:
mincRayTraceStats(v,"/some/path/anatomical.mnc", vs[,3], like.filename = attr(vs, "likeVolume"))
# or
mincRayTraceStats(v,"/some/path/anatomical.mnc", vs, column = 3)

## End(Not run)

Mouse-Imaging-Centre/RMINC documentation built on Nov. 12, 2022, 1:50 p.m.