Segmentation UNSURE

This programs aims to evaluate segmentation using as much as possible linux basic utilities.

Requirements

• linux (tested on Arch Linux)
• GNU make (tested with version 4.4.1)
• sxiv (tested with version v26-1-g2cac112)
• itksnap (tested with version 3.8.0)
• notify-send (0.8.2)

How to run

Configuration

• Change adequately and consistently the variables IN and OUT in both Makefile and key-handler
• PLACE YOURSELF IN A NEW PYTHON VIRTUALENV, and run:

make set

Preprocess of the data

Run the preprocessing in parallel (-j4 means 4 jobs in parallel):

make -j4 preprocess

Run

Run the processing (based on sxiv and itksnap)

make process

Clean

Clean the directory

make clean

TIPS

SXIV shortcut

• most vim shortcuts
• <cr> switch between thumbnail and image mode
• + zoom in
• - zoom out
• n next image
• p previous image
• C-x C-j okay
• C-x C-k not okay
• C-x C-v vizualize the image in itksnap

TODO

• make the pre-processing of the ground-truth to reduce there size
• Change itksnap for a python code

Author

Robin Camarasa