segment Visceral and Subcutaneous Adipose Tissue (VAT, SAT) in water-fat MRI images
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README.md

Description

vatsatseg is a python implementation of the matlab segmentation tool "SAT_VAT_segmentation" used in

Shen, J., Baum, T., Cordes, C., Ott, B., Skurk, T., Kooijman, H., Rummeny, E. J., …, Automatic segmentation of abdominal organs and adipose tissue compartments in water-fat mri: application to weight-loss in obesity, European Journal of Radiology, 85(9), 1613–1621 (2016). http://dx.doi.org/10.1016/j.ejrad.2016.06.006

Installation

You can install vatsatseg by typing the following commands in your terminal:

git clone https://github.com/maxdiefenbach/vatsatseg # clone project

cd vatsatseg                    # change directory

pip install -e .                # install package

This automatically installs the commandline tool "$ vatsatseg".

Dependency

To manually correct the segmentation result vatsatseg relies on ITK-SNAP. By invoking the "–show" option, the water and fat images together with the segmentation overlay will be open. For this you need to make sure the "viewer command" in the configuration file "vatsatseg/config.ini" points to the correct installation path of ITK-SNAP.

Tutorial

see help

vatsatseg --help

Usage: vatsatseg [OPTIONS]

  segment Visceral and Subcutaneous Adipose Tissue (VAT, SAT) in water-fat
  MRI images

Options:
  -w, --water PATH   Water MRI image file.
  -f, --fat PATH     Fat MRI image file.
  -o, --output PATH  Output label map file name.
  --peel INTEGER     Number of voxels of the subcutaneous fat ring thickness.
                     [default: 10]
  -s, --show         Open ITK-SNAP to manually correct the labelmap.
  -h, --help         Show this message and exit.

example

vatsatseg -w t1_vibe_dixon_tra_lower_W.nii \
          -f t1_vibe_dixon_tra_lower_F.nii \
          -o vat_sat_seg.nii \
          -s

Tutorial

see help

python vatsatseg.py --help

example

python vatsatseg.py \
       -w t1_vibe_dixon_tra_lower_W.nii \
       -f t1_vibe_dixon_tra_lower_F.nii \
       -o vat_sat_seg.nii \
       -s

Contact

vatsatseg is in an early development state. We are happy about feedback and/or contributions on Github.

Report bugs / Request Features

If you can report a bug or would like to request a feature, please create an issue here.

Contribute

If you can contribute we are happy about pull or merge requests on Github.

License

vatsatseg, segment visceral and subcutaneous adipose tissue Copyright (C) 2018 Maximilian N. Diefenbach

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Acknowlegment

vatsatseg is developed in the Body Magnetic Resonance Research Group at the Klinikum rechts der Isar and the Technical University Munich.