Skeletonise NRRD images (e.g. to make them suitable for NBLAST)

skeletonise_nrrds(
  input,
  outdir,
  threshold = 0,
  threshold.first = FALSE,
  fileregex = NULL,
  DryRun = TRUE,
  ...
)

Arguments

input	Path to single input file or an input directory
outdir	Path to output directory
threshold	Integer specifying an absolute threshold or string specifying ImageJ authothreshold method.
threshold.first	Whether to threshold the image before rescaling. This is a good idea if you have mask images (especially 0-1 masks) as your input. (default: `FALSE`)
fileregex	Optional regex matching the whole of the filename (NB just filename without parent directory)
DryRun	Show what would happen but don't run (default TRUE)
...	Additional arguments passed to `runFijiMacro`

Value

Logical indicating if the command completed successfully

Examples

if (FALSE) {
# basic version
skeletonise_nrrds('/path/to/indir', '/path/to/outdir')
# convert those to dotrops for NBLAST
dps=dotprops(dir('/path/to/outdir', pattern='nrrd$', full.names=TRUE))

# additional arguments
skeletonise_nrrds('/path/to/indir', '/path/to/outdir', threshold='Iso_Data')
skeletonise_nrrds('/path/to/indir', '/path/to/outdir', fileregex='^seg_whole.*c0\\.nrrd')
}