A utility function to give a MINC object spatial dimensions

Currently the plotting functions (mincPlotAnatAndStatsSlice) need an object with the correct spatial dimensions assigned. While this might in the future happen at the time those objects are created, for the moment this utility function works with older style RMINC objects and extract what you need.

Usage

mincArray(volume, dimIndex = 1, maskVolume = NULL)

Arguments

volume: The input volume (from mincLm, mincGetVolume, etc.)
dimIndex: The index into a multidimensional object
maskVolume: The optional mask from which the data was created

Value

A matrix with 3 dimensions

Details

At times data is computed within a mask; for example mincTable matrices can be extracted from masked data. In that case if the mask volume is passed as an argument then the data will will be reinserted into those parts of the mask volume greater than zero.

Note

R uses Fortran indexing, so dimension assignment is c(dim[3], dim[2], dim[1]) once dimensions are obtained from any libminc functions (which use C indexing)

Examples

if (FALSE) { # \dontrun{
vol <- mincGetVolume("somefile.mnc")
volWithDims <- mincArray(vol)

vs <- mincLm(jacobians ~ genotype, gf)
tvol <- mincArray(vs, 6)
} # }