SPM BWLabel Clusters of Certain Size — spm

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
)

Arguments

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

Value

Output from run_matlab_script or nifti object, depending on retimg

Result from run_matlab_script

Note

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

Examples

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, install_dir = tempdir())
tab = table(c(res))
tab
out_arr = as(res, "array")
}
#> cloning into '/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//Rtmp13birO/spm12'...
#> Receiving objects:   1% (68/6722),   23 kb
#> Receiving objects:  11% (740/6722), 2964 kb
#> Receiving objects:  21% (1412/6722), 3316 kb
#> Receiving objects:  31% (2084/6722), 9469 kb
#> Receiving objects:  41% (2757/6722), 10987 kb
#> Receiving objects:  51% (3429/6722), 31461 kb
#> Receiving objects:  61% (4101/6722), 36479 kb
#> Receiving objects:  71% (4773/6722), 46980 kb
#> Receiving objects:  81% (5445/6722), 70570 kb
#> Receiving objects:  91% (6118/6722), 99259 kb
#> Receiving objects: 100% (6722/6722), 131273 kb, done.
#> # K = 1
#> # Script is located at /var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//Rtmp13birO/file9be853c26c6.m
#> Command run is:
#> matlab  -nodesktop -nosplash   -nodisplay -r  "try, run('/var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//Rtmp13birO/file9be853c26c6.m'); catch err, disp(err.message); exit(1); end; exit(0);"
#> # Reading output file /var/folders/1s/wrtqcpxn685_zk570bnx9_rr0000gr/T//Rtmp13birO/file9be874478c0e.nii
#>