usages:
directory is the pathname of a directory that contains subdirectories named `pd' and `t2', which in turn contain the proton density and T2-weighted image sets, respectively. These sets should consist of files in RLE (.bw) format, named as slice numbers, starting with `1.bw' (or `01.bw' or `001.bw'). The same zero-padding convention should be used in all these file names.
To accomplish its work, segment calls model, siscale, correct, and 3dseg. Inside directory, these programs create the files `2dhistck.bw', `parameters.dat', and `scale.dat', and the subdirectories `pdc', `t2c', `seg', and `seg2'. The standard output of these programs is saved in `segment.out', and the standard error is saved in `segment.err'.
If given the `-f' option, segment will overwrite any old segmentation data that appear in directory. Otherwise, the presence of old data causes segment to abort.
Since segmentation can take quite a long time to complete, segment runs in the background. This allows the user to log out without causing the program to terminate. If given the `-i' option, segment will remain in interactive mode until it has finished computing the segmentation parameters, and ask the user to approve these before proceeding.
Author of segment interface: Matthew Belmonte
Author of model, siscale, correct, and 3dseg: Brian Egaas