vertexApply: Apply function over vertex Files

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

Apply function over vertex Files

Description

This function is used to compute an arbitrary function of every region in a set of vertex files.

Usage

vertexApply(
  filenames,
  fun,
  ...,
  mask = NULL,
  parallel = NULL,
  collate = simplify_masked,
  transpose = FALSE,
  column = 1
)

Arguments

filenames	vertex file names
fun	A function to be applied to each vertex
...	additional arguments to fun
mask	A vector of filename indicating a vertex mask (fun is applied to all vertices where mask is greater than .5)
parallel	A two component vector indicating how to parallelize the computation. If the first element is "local" the computation will be run via the parallel package, otherwise it will be computed using batchtools, see pMincApply for details. The element should be numeric indicating the number of jobs to split the computation into.
collate	A function to reduce the (potentially masked) list of results into a nice structure. Defaults to simplify_masked
transpose	Whether to alternatively transpose the vertex matrix and apply a function to each subject
column	Which column to treat as the input from vertex files.

Value

The a matrix with a row of results for each vertex

Examples

## Not run: 
getRMINCTestData() 
gf = read.csv("/tmp/rminctestdata/CIVET_TEST.csv")
gf = civet.getAllFilenames(gf,"ID","TEST","/tmp/rminctestdata/CIVET","TRUE","1.1.12")
gf = civet.readAllCivetFiles("/tmp/rminctestdata/AAL.csv",gf)
vm <- vertexApply(gf$CIVETFILES$nativeRMStlink20mmleft, mean)

## End(Not run)

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