Containerized implementation of SynthSeg with additional preprocessing options
Containers are available on DockerHub
https://github.com/cookpa/SynthSegContainer - go here if you want to build SynthSeg that just runs the built-in prediction script.
This container uses SynthSeg, please see its license and cite the appropriate papers.
The authors ask that if it is used in published research, to cite:
SynthSeg: Domain Randomisation for Segmentation of Brain MRI Scans of any Contrast and Resolution B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A.V. Dalca, J.E. Iglesias (https://pubmed.ncbi.nlm.nih.gov/36857946/)
For cortical parcellation, automated QC, or robust fitting, please also cite the following paper:
Robust Segmentation of Brain MRI in the Wild with Hierarchical CNNs and no Retraining B. Billot, M. Colin, S.E. Arnold, S. Das, J.E. Iglesias MICCAI 2022