Description Usage Arguments Value Examples
Skeletonise NRRD images (e.g. to make them suitable for NBLAST)
1 2 3 4 5 6 7 8 9 | skeletonise_nrrds(
input,
outdir,
threshold = 0,
threshold.first = FALSE,
fileregex = NULL,
DryRun = TRUE,
...
)
|
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: |
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 |
Logical indicating if the command completed successfully
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
# 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')
## End(Not run)
|
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