Fetal brain surface generation from deep learning labels
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Note: this is a preliminary version for testing purposes only (01/2024) based on the optimised surface generation scripts from https://github.com/MIRTK/DrawEM (A. Makropoulos, E. C. Robinson et al. "The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction", NeuroImage, 2018).
The script does not require Draw-EM outputs and uses deep learning fetal brain segmentations as an input instead.
The source code repository: https://github.com/SVRTK/surface-svrtk
Pull the docker image:
docker pull fetalsvrtk/surface:1.40
Run the docker mounted to the folder with .nii.gz files for processing:
docker run -it --rm --mount type=bind,source=location_on_your_machine,target=/home/data fetalsvrtk/surface:1.40 /bin/bash
Run surface reconstruction for the fetal brain:
Please note that it requires a T2w 3D SVR reconstructed image and brain segmentation files (BOUNTI, BET, CC).
cd /home/data
bash /software/surface-scripts/bounti-surface-generation-v3-tissue-internal.sh sub-000_ses-000 /home/data/test/test-0000.nii.gz /home/data/test/test-0000-mask-brain_dhcp-19.nii.gz /home/data/test/test-0000-mask-brain_bet-1.nii.gz /home/data/test/test-0000-mask-brain_cc-2.nii.gz /home/data/proc-test 0
For new multi-ROI BOUNTI with 47 labels use this command:
cd /home/data
bash /software/surface-scripts/bounti-surface-generation-v4-multi-internal.sh sub-000_ses-000 /home/data/test/test-0000.nii.gz /home/data/test/test-0000-mask-brain_dhcp-47.nii.gz
/home/data/proc-test 0
The MIRTK SVRTK package is distributed under the terms of the Apache License Version 2. The license enables usage of SVRTK in both commercial and non-commercial applications, without restrictions on the licensing applied to the combined work.
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.
In case you found SVRTK useful please give appropriate credit to the software:
SVRTK surface dockers: https://hub.docker.com/r/fetalsvrtk/surface
SVRTK segmentation dockers: https://hub.docker.com/r/fetalsvrtk/segmentation
Makropoulos A, Robinson EC, Schuh A, Wright R, Fitzgibbon S, Bozek J, Counsell SJ, Steinweg J, Vecchiato K, Passerat-Palmbach J, Lenz G, Mortari F, Tenev T, Duff EP, Bastiani M, Cordero-Grande L, Hughes E, Tusor N, Tournier JD, Hutter J, Price AN, Teixeira RPAG, Murgasova M, Victor S, Kelly C, Rutherford MA, Smith SM, Edwards AD, Hajnal JV, Jenkinson M, Rueckert D. The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction. Neuroimage. 2018 Jun;173:88-112. doi: https://doi.org/10.1016/j.neuroimage.2018.01.054.
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. eLife12:RP88818; doi: https://doi.org/10.1101/2023.04.18.537347
Content type
Image
Digest
sha256:cee9592fe…
Size
3.3 GB
Last updated
8 days ago
docker pull fetalsvrtk/surface:multi_bounti_2026