spm_bwlabel: SPM BWLabel Clusters of Certain Size
In neuroconductor-devel/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

Description Usage Arguments Value Note Examples

Get Cluster of certain size from spm_bwlabel

spm_bwlabel(infile, outfile = NULL, retimg = TRUE, k = NULL,
  topN = NULL, margin = NULL, binary = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  reorient = FALSE, verbose = TRUE, install_dir = NULL)

`infile`	input filename
`outfile`	output filename
`retimg`	Return the image instead of matlab output
`k`	Minimum cluster size needed
`topN`	Top number of clusters kept (used if k is `NULL`)
`margin`	Margin to loop over if wanted in 2D
`binary`	(logical) Should the result be binary or numbered with cluster.
`spmdir`	SPM directory (for MATLAB)
`reorient`	If `retimg`, then this argument is passed to `readNIfTI`
`verbose`	Print Diagnostics
`install_dir`	directory to download SPM12

Output from run_matlab_script or nifti object, depending on retimg

Result from run_matlab_script

Taken from http://en.wikibooks.org/wiki/SPM/How-to#How_to_remove_clusters_under_a_certain_size_in_a_binary_mask.3F

if (matlabr::have_matlab()) { 
d = rep(25, 3)
arr = array(rbinom(prod(d), size = 1, prob = 0.5), dim = d)
nim = oro.nifti::nifti(arr)
res = spm_bwlabel(nim, k = 1, binary = FALSE)
tab = table(c(res))
tab
out_arr = as(res, "array")
}