Abstract
Fetal functional magnetic resonance imaging (fMRI) offers critical insight into the developing brain and could aid in predicting developmental outcomes. As the fetal brain is surrounded by heterogeneous tissue, it is not possible to use adult- or child-based segmentation toolboxes. Manually-segmented masks can be used to extract the fetal brain; however, this comes at significant time costs. Here, we present a new BIDS App for masking fetal fMRI, funcmasker-flex, that overcomes these issues with a robust 3D convolutional neural network (U-net) architecture implemented in an extensible and transparent Snakemake workflow. Open-access fetal fMRI data with manual brain masks from 159 fetuses (1103 total volumes) were used for training and testing the U-net model. We also tested generalizability of the model using 82 locally acquired functional scans from 19 fetuses, which included over 2300 manually segmented volumes. Dice metrics were used to compare performance of funcmasker-flex to the ground truth manually segmented volumes, and segmentations were consistently robust (all Dice metrics ≥ 0.74). The tool is freely available and can be applied to any BIDS dataset containing fetal bold sequences. Funcmasker-flex reduces the need for manual segmentation, even when applied to novel fetal functional datasets, resulting in significant time-cost savings for performing fetal fMRI analysis.
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Acknowledgements
The authors would like to thank the women who participated in these studies. We also thank the researchers at WS/YU for making their data and code available. We thank Megan Mueller, Sarah Abu Al-Saoud, Tajveer Ubhi, and Alissa Papadopolous for their assistance with manually tracing the fetal MRI data, and David Reese for his assistance in collecting the fetal MRI data.
Funding
The funding for this research was provided by the Canadian Institutes of Health Research, the Molly Towell Perinatal Health Foundation and the Canada First Research Excellence Fund by BrainsCAN.
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Nichols, E.S., Correa, S., Van Dyken, P. et al. Funcmasker-flex: An Automated BIDS-App for Brain Segmentation of Human Fetal Functional MRI data. Neuroinform 21, 565–573 (2023). https://doi.org/10.1007/s12021-023-09629-3
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DOI: https://doi.org/10.1007/s12021-023-09629-3