Fetpype is a pipeline for processing in vivo human fetal brain MRI

This pipeline is the fruit of a collaborative effort shared across teams involved in the ERANET MultiFact project. Fetpype is in active development, contributions and feedback are very warmly welcome.

Fetpype is a library that aims at facilitating the analysis of fetal brain MRI by integrating the variety of tools commonly used in processing pipelines. Starting from clinical acquisition of fetal brain MRI (T2-weighted fast spin echo sequences), it performs pre-processing, reconstruction, segmentation and surface extraction (to be implemented).

It aims at making easy the integration of a variety of tools existing to process fetal brain MR images by providing a wrapper around docker/singularity containers and working with BIDS formatted data.

More information are available on the documentation.

If you use Fetpype in your research, please cite the following paper:

@article{sanchez2025fetpype,
  title={Fetpype: An open-source pipeline for reproducible fetal brain mri analysis},
  author={Sanchez, Thomas and Mart{\'\i}-Juan, Gerard and Meunier, David and Ballester, Miguel Angel Gonzalez and Camara, Oscar and Piella, Gemma and Cuadra, Meritxell Bach and Auzias, Guillaume},
  journal={arXiv preprint arXiv:2512.17472},
  year={2025}
}