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

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) # }