em

Synopsis

em <input> <N> <prob1> .. <probN> <output> [options]

Description

Runs EM segmentation at the input image with the provided N probability maps of structures. e.g. em input.nii.gz 5 bg.nii.gz csf.nii.gz gm.nii.gz wm.nii.gz dgm.nii.gz segmentation.nii.gz

Input options

-mask <mask>

run EM inside the provided mask

-padding <number>

run EM where input > padding value

-iterations <number>

maximum number of iterations (default: 50)

-saveprob <number> <file> save posterior probability of structure with number <number> to file

(0-indexed i.e. structure 1 has number 0)

-saveprobs <basename>

save posterior probability of structures to files with basename <basename>

Standard options

-v, -verbose [n]

Increase/Set verbosity of output messages. (default: 0)

-debug [level]

Increase/Set debug level for output of intermediate results. (default: 0)

-version [major.minor]

Print version and exit or set version to emulate.

-revision

Print revision (or version) number only and exit.

-h, -help

Print help and exit.