Example code and data for the techniques discussed in Tustison et al., Atlas-based estimation of lung and lobar anatomy in proton MRI. Magn Reson Med.
- Need to run it through twice as discussed in the paper. The first run is to simply extract the lungs which gives a better registration for the second round.
- Download and install ANTs.
- Add the ANTs binary directory to your path environment variable.
- Run
exampleLungLobeEstimation.shfrom theLungandLobeEstimationExample/directory.
Evaluation
Lung mask estimation label overlap measures
************ All Labels *************
Total Union (jaccard) Mean (dice) Volume sim. False negative False positive
0.978303 0.956787 0.977916 0.000791194 0.0216966 0.0224703
************ Individual Labels *************
Label Target Union (jaccard) Mean (dice) Volume sim. False negative False positive
1 0.975608 0.959328 0.979242 -0.00745017 0.0243923 0.0170967
2 0.981569 0.953745 0.976325 0.0106853 0.0184308 0.0288635
Lobe mask estimation label overlap measures
************ All Labels *************
Total Union (jaccard) Mean (dice) Volume sim. False negative False positive
0.956222 0.911176 0.953524 0.00564215 0.0437785 0.0491584
************ Individual Labels *************
Label Target Union (jaccard) Mean (dice) Volume sim. False negative False positive
1 0.963516 0.919172 0.957884 0.0116906 0.0364842 0.0476829
2 0.970837 0.927132 0.962188 0.0178171 0.0291631 0.0463078
3 0.919346 0.900792 0.947807 -0.061917 0.0806545 0.0219128
4 0.966887 0.855415 0.922074 0.0926963 0.0331126 0.118769
5 0.9711 0.917791 0.957133 0.0287653 0.0288997 0.0564376