SMILEUHURA_DS6_UNetMSS3D_wDeform

Baseline model from the vessel segmentation challenge: SMILE-UHURA (https://doi.org/10.7303/syn47164761) and the research paper SPOCKMIP.

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer’s disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi’s vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 ± 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98%) with deformation-aware learning.

Model Details

It was introduced in DS6, Deformation-Aware Semi-Supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data by Soumick Chatterjee, Kartik Prabhu, Mahantesh Pattadkal, Gerda Bortsova, Chompunuch Sarasaen, Florian Dubost, Hendrik Mattern, Marleen de Bruijne, Oliver Speck, Andreas Nürnberger. ArXiv preprint

The model architecture is the same as the original paper, but it was trained on the SMILE-UHURA dataset. This model was used as a baseline model at the SMILE-UHURA challenge (https://doi.org/10.7303/syn47164761) and as well as in the research paper SPOCKMIP: Segmentation of Vessels in MRAs with Enhanced Continuity using Maximum Intensity Projection as Loss.

Model Description

• Model type: UNet Multi-scale Supervision (UNet-MSS) 3D
• Task: Vessel segmentation in 7T MRA-ToF volumes
• Training dataset: 7T ToF-MRAs from the vessel segmentation challenge: SMILE-UHURA (https://doi.org/10.7303/syn47164761)
• Training type: Trained with deformation-aware learning (Proposed DS6 method)

Model Sources

Original DS6:

• Repository: https://github.com/soumickmj/DS6
• Paper: https://doi.org/10.3390/jimaging8100259
• Preprint: https://arxiv.org/abs/2006.10802

SPOCKMIP:

• Repository: https://github.com/soumickmj/SPOCKMIP
• Preprint: https://arxiv.org/abs/2407.08655

Citation

If you use this approach in your research or use codes from this repository or these weights, please cite all the following in your publications:

BibTeX:

DS6:

@article{chatterjee2022ds6,
  title={Ds6, deformation-aware semi-supervised learning: Application to small vessel segmentation with noisy training data},
  author={Chatterjee, Soumick and Prabhu, Kartik and Pattadkal, Mahantesh and Bortsova, Gerda and Sarasaen, Chompunuch and Dubost, Florian and Mattern, Hendrik and de Bruijne, Marleen and Speck, Oliver and N{\"u}rnberger, Andreas},
  journal={Journal of Imaging},
  volume={8},
  number={10},
  pages={259},
  year={2022},
  publisher={MDPI}
}

SPOCKMIP:

@article{radhakrishna2024spockmip,
  title={SPOCKMIP: Segmentation of Vessels in MRAs with Enhanced Continuity using Maximum Intensity Projection as Loss},
  author={Radhakrishna, Chethan and Chintalapati, Karthikesh Varma and Kumar, Sri Chandana Hudukula Ram and Sutrave, Raviteja and Mattern, Hendrik and Speck, Oliver and N{\"u}rnberger, Andreas and Chatterjee, Soumick},
  journal={arXiv preprint arXiv:2407.08655},
  year={2024}
}

SMILE-UHURA:

https://doi.org/10.7303/syn47164761

APA:

Chatterjee, S., Prabhu, K., Pattadkal, M., Bortsova, G., Sarasaen, C., Dubost, F., ... & Nürnberger, A. (2022). Ds6, deformation-aware semi-supervised learning: Application to small vessel segmentation with noisy training data. Journal of Imaging, 8(10), 259.

Radhakrishna, C., Chintalapati, K. V., Kumar, S. C. H. R., Sutrave, R., Mattern, H., Speck, O., ... & Chatterjee, S. (2024). SPOCKMIP: Segmentation of Vessels in MRAs with Enhanced Continuity using Maximum Intensity Projection as Loss. arXiv preprint arXiv:2407.08655.

https://doi.org/10.7303/syn47164761