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")
| 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. |
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], 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) # }