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
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".
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.
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.
vatsatseg -w t1_vibe_dixon_tra_lower_W.nii \ -f t1_vibe_dixon_tra_lower_F.nii \ -o vat_sat_seg.nii \ -s
python vatsatseg.py --help
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
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.
If you can contribute we are happy about pull or merge requests on Github.
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/.