Outline of Torso Segmentation Problem

Torso Segmentation

We currently take CT scans with vascular contrast and segment them into individual tissues. Each one of these tissues is segmented utilizing different tools within Slicer. Each label is then hierarchically combined using the unu command line tool in the TEEM toolkit developed by Gordon Kindlmann.

We segment the following tissues: Bounding box, torso(shadow), bowelgas, muscle, fat, liver, kidneys, lung, bone, blood, heart

We then use the unu tool to combine individual tissue which are labeled 1 with a background of 0 with the following command:

unu 2op x 0 29y-85kgbbox.nrrd -o max.nrrd

unu 2op x 1 29y-85kgtorso1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 2 29y-85kgbowelgas1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 3 29y-85kgmuscle1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 4 29y-85kgfat1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 5 29y-85kgliver1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 6 29y-85kgkidneys1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 7 29y-85kglung1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 8 29y-85kgbone1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 9 29y-85kgblood1-0.nrrd | unu 2op max max.nrrd - -o max.nrrd

unu 2op x 10 29y-85kgheart1-0.nrrd | unu 2op max max.nrrd - -o 29y-75kgcombined.nrrd