Implementation of a TorchIO transform used to simulate a resection cavity from a T1-weighted brain MRI and a corresponding geodesic information flows (GIF) brain parcellation (version 3.0).
If you use this library for your research, please cite our MICCAI 2020 paper:
Bibtex:
@InProceedings{10.1007/978-3-030-59716-0_12,
author="P{\'e}rez-Garc{\'i}a, Fernando
and Rodionov, Roman
and Alim-Marvasti, Ali
and Sparks, Rachel
and Duncan, John S.
and Ourselin, S{\'e}bastien",
title="Simulation of Brain Resection for Cavity Segmentation Using Self-supervised and Semi-supervised Learning",
booktitle="Medical Image Computing and Computer Assisted Intervention -- MICCAI 2020",
year="2020",
publisher="Springer International Publishing",
address="Cham",
pages="115--125",
isbn="978-3-030-59716-0"
}$ git clone https://github.com/fepegar/resector.git
$ pip install --editable ./resector$ resect t1.nii.gz gif_parcellation.nii.gz t1_resected.nii.gz t1_resection_label.nii.gzRun resect --help for more options.