Publications

Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study

Kebiri, H., Gholipour, A., Vasung, L., Calixto, C., Krsnik, Z., Karimi*, D., Bach Cuadra*, M. (2024). "Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study." Medical Image Analysis.

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Functional organization of the neonatal thalamus across development depicted by functional MRI

Kebiri, H., Delavari, F., Van De Ville, D., Jorge*, J., Bach Cuadra*, M. (2025). "Functional organization of the neonatal thalamus across development depicted by functional MRI." Imaging Neuroscience.

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Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain

Kebiri, H., Canales-Rodriguez, E.J., Lajous, H., de Dumast, P., Girard, G., Aleman-Gomez, Y., Koob, M., Jakab, A., Bach Cuadra, M. (2021). "Through-plane super-resolution with autoencoders in diffusion magnetic resonance imaging of the developing human brain." Frontiers in Neurology.

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Domain shifts in infant brain diffusion MRI: Quantification and mitigation for fODF estimation

Kebiri*, H., Lin*, R., Gholipour, A., Chen, Y., Thiran, J.P., Karimi, D., Bach Cuadra, M. (2025). "Domain shifts in infant brain diffusion MRI: Quantification and mitigation for fODF estimation." Human Brain Mapping.

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RimNet: A deep 3D multimodal MRI architecture for paramagnetic rim lesions assessment in multiple sclerosis

Barquero Garcia, G., La Rosa, F., Kebiri, H., et al. (2020). "RimNet: A deep 3D multimodal MRI architecture for paramagnetic rim lesions assessment in multiple sclerosis." NeuroImage: Clinical.

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Multi-view convolutional neural networks for automated ocular structure and tumor segmentation in retinoblastoma

Strijbis, V.I.J., de Bloeme, C.M., Jansen, R.W., Kebiri, H., et al. (2021). "Multi-view convolutional neural networks for automated ocular structure and tumor segmentation in retinoblastoma." Nature Scientific Reports.

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An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset

Payette, K., de Dumast, P., Kebiri, H., et al. (2022). "An automatic multi-tissue human fetal brain segmentation benchmark using the Fetal Tissue Annotation Dataset." Nature Scientific Data.

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Learning environments are associated withdevelopmental trajectories of thalamocorticalattention circuits in childhood (submitted)

Mino-Matot*, T., Kebiri*, H. Jorge, J., Ledoux, J.B., Fornari, E., Bach Cuadra, M., Denervaud, S. (2026). "Data-driven pediatric thalamic parcellation reveals pedagogy-selective maturation of attention circuits."

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Multi-dimensional topological loss for cortical plate segmentation in fetal brain MRI

de Dumast, P., Kebiri, H., Dunet, V., Koob, M., Bach Cuadra, M. (2022). "Multi-dimensional topological loss for cortical plate segmentation in fetal brain MRI." arXiv.

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Robust estimation of the microstructure of the early developing brain using deep learning

Kebiri, H., Gholipour, A., Lin, R., Vasung, L., Karimi*, D., Bach Cuadra*, M. (2023). "Robust estimation of the microstructure of the early developing brain using deep learning." MICCAI, Vancouver, Canada.

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Cross-Age and Cross-Site Domain Shift Impacts on Deep Learning-Based White Matter Fiber Estimation in Newborn and Baby Brains

Lin, R., Gholipour, A., Karimi, D., Thiran, J.P., Kebiri*, H., Bach Cuadra*, M. (2024). "Cross-Age and Cross-Site Domain Shift Impacts on Deep Learning-Based White Matter Fiber Estimation in Newborn and Baby Brains." IEEE ISBI, Athens, Greece.

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Spatio-temporal motion correction and iterative reconstruction of in-utero fetal fMRI

Taymourtash, A., Kebiri, H., Schwartz, E., Nenning, K.H., Tourbier, S., Kasprian, G., Prayer, D., Bach Cuadra, M., Langs, G. (2022). "Spatio-temporal motion correction and iterative reconstruction of in-utero fetal fMRI." MICCAI, Singapore.

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Improving cross-domain brain tissue segmentation in fetal MRI with synthetic data

Zalevskyi, V., Sanchez, T., Roulet, M., Aviles Verddera, J., Hutter, J., Kebiri, H., Bach Cuadra, M. (2024). "Improving cross-domain brain tissue segmentation in fetal MRI with synthetic data." MICCAI, Marrakesh, Morocco.

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Direct segmentation of brain white matter tracts in diffusion MRI

Kebiri, H., Gholipour, A., Bach Cuadra, M., Karimi, D. (2023). "Direct segmentation of brain white matter tracts in diffusion MRI." arXiv.

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TBSS++: A novel computational method for Tract-Based Spatial Statistics

Karimi, D., Kebiri, H., Gholipour, A. (2023). "TBSS++: A novel computational method for Tract-Based Spatial Statistics." arXiv.

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Uncertainty-Aware Functional Parcellation of the Neonatal Thalamus Using a Large dHCP rs-fMRI Cohort (abstract)

Kebiri, H., Delavari, F., Van De Ville, D., Jorge, J., Bach Cuadra, M. (2025). "Uncertainty-Aware Functional Parcellation of the Neonatal Thalamus Using a Large dHCP rs-fMRI Cohort." OHBM, Brisbane, Australia.