mincRayTraceStats {RMINC} | R Documentation |
Takes a voxel, an anatomical file, and a statistics file to create an image of the statistical peak.
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)
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. |
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.
mincLm, mincFDR, mincMean, mincSd
## 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)