This repository is used for storage / log of scripts for automated processing of fetal MRI in SVRTK dockers as well as general processing for:
- segmentation
- SVR-based reconstruction
Note: The scripts were installed in the corresponding docker containers together with network weights and SVRTK software. I.e., they cannot be used as standalone applications and need to be executed from the dockers.
The repository and code were created by Dr Alena Uus.
Development of SVRTK was supported by projects led by Dr Maria Deprez, Prof Mary Rutherford, Dr Jana Hutter, Dr Lisa Story and Prof Jo Hajnal.
The auto SVRTK code and all scripts are distributed under the terms of the GNU General Public License v3.0. 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. 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.
In case you found SVRTK useful please give appropriate credit to the software (SVRTK dockers).
Uus, A. U., Hall, M., Payette, K., Hajnal, J. V., Deprez, M., Hutter, J., Rutherford, M. A., Story, L. (2023) Combined quantitative T2* map and structural T2- weighted tissue-specific analysis for fetal brain MRI: pilot automated pipeline. PIPPI MICCAI 2023 workshop (Accepted / in press)
Uus, A., Grigorescu, I., van Poppel, M., Steinweg, J. K., Roberts, T., Rutherford, M., Hajnal, J., Lloyd, D., Pushparajah, K. & Deprez, M. (2022) Automated 3D reconstruction of the fetal thorax in the standard atlas space from motion-corrupted MRI stacks for 21-36 weeks GA range. Medical Image Analysis, 80 (August 2022).: https://doi.org/10.1016/j.media.2022.102484
Uus, A. U., Kyriakopoulou, V., Makropoulos, A., Fukami-Gartner, A., Cromb, D., Davidson, A., Cordero-Grande, L., Price, A. N., Grigorescu, I., Williams, L. Z. J., Robinson, E. C., Lloyd, D., Pushparajah, K., Story, L., Hutter, J., Counsell, S. J., Edwards, A. D., Rutherford, M. A., Hajnal, J. V., Deprez, M. (2023) BOUNTI: Brain vOlumetry and aUtomated parcellatioN for 3D feTal MRI. bioRxiv 2023.04.18.537347; doi: https://doi.org/10.1101/2023.04.18.537347
Uus, A. U., Hall, M., Grigorescu, I., Avena Zampieri, C., Egloff Collado, A., Payette, K., Matthew, J., Kyriakopoulou, V., Hajnal, J. V., Hutter, J., Rutherford, M. A., Deprez, M., Story, L. (2023) Automated body organ segmentation and volumetry for 3D motion-corrected T2-weighted fetal body MRI: a pilot pipeline. medRxiv 2023.05.31.23290751; doi: https://doi.org/10.1101/2023.05.31.23290751
This software has been developed for research purposes only, and hence should not be used as a diagnostic tool. In no event shall the authors or distributors be liable to any direct, indirect, special, incidental, or consequential damages arising of the use of this software, its documentation, or any derivatives thereof, even if the authors have been advised of the possibility of such damage.