ITK-SNAP brings active contour segmentation to the fingertips of clinical researchers. This application fulfills a specific and pressing need of biomedical imaging research by providing a combination of manual and semiautomatic tools for extracting structures in 3D image data of different modalities and from different anatomical regions.

References:

• Paul A. Yushkevich, Joseph Piven, Heather Cody Hazlett, Rachel Gimpel Smith, Sean Ho, James C. Gee and Guido Gerig
  User-guided 3D active contour segmentation of anatomical structures: Significantly improved efficiency and reliability.
  NeuroImage 31 (2006) 1116 – 1128

• ITK-SNAP-Burgess-Sodt Github page
• ITK-snap-builder Github page
• ITK-SNAP Documentation

• Module Name: ITK-SNAP-BS (see the modules page for more information)
• Unusual environment variables set
  • IS_HOME  home folder
  • IS_BIN   executable folder
  • IS_SRC   source folder

As the first step, please allocate an interactive session:

The use of ITK-SNAP-BS GUI requires a graphical X11 connection.
Both NX and MobaXterm work well for Windows users,
while XQuartz works well for Mac users.

[user@biowulf]$ sinteractive --gres=gpu:p100:1,lscratch:10 --mem=20g -c14
[user@cn4469 ~]$ module load DeepLabCut/2.2.2 
[+] Loading singularity  3.10.5  on cn0825
[+] Loading ITK-SNAP-BS  20131007

[user@cn4469 user]$ itksnap