The following examples illustrate the intended use of pymia:
The examples are available as Jupyter notebooks and Python scripts on GitHub or directly rendered in the documentation by following the links above. Furthermore, there exist complete training scripts in TensorFlow and PyTorch at ./examples/training-examples on GitHub. For all examples, 3 tesla MR images of the head of four healthy subjects from the Human Connectome Project (HCP) [VanEssen2013] are used. Each subject has four 3-D images (in the MetaImage and Nifty format) and demographic information provided as a text file. The images are a T1-weighted MR image, a T2-weighted MR image, a label image (ground truth), and a brain mask image. The demographic information is artificially created age, gender, and grade point average (GPA). The label images contain annotations of five brain structures (1: white matter, 2: grey matter, 3: hippocampus, 4: amygdala, and 5: thalamus [0 is background]), automatically segmented by FreeSurfer 5.3 [Fischl2012] [Fischl2002]. Therefore, the examples mimic the problem of medical image segmentation of brain tissues.
Projects using pymia¶
pymia was used for several projects, which have public code available and can serve as an additional point of reference complementing the documentation. Projects using version >= 0.3.0 are:
Spatially Regularized Parametric Map Reconstruction for Fast Magnetic Resonance Fingerprinting: Code for the Medical Image Analysis paper by Balsiger et al. with data handling and evaluation.
Learning Bloch Simulations for MR Fingerprinting by Invertible Neural Networks: Code for the MLMIR 2020 paper by Balsiger and Jungo et al. with evaluation.
Medical Image Analysis Laboratory: Code for a MSc-level lecture at the University of Bern with image filtering and evaluation.
Van Essen, D. C., Smith, S. M., Barch, D. M., Behrens, T. E. J., Yacoub, E., Ugurbil, K., & WU-Minn HCP Consortium. (2013). The WU-Minn Human Connectome Project: An overview. NeuroImage, 80, 62–79. https://doi.org/10.1016/j.neuroimage.2013.05.041
Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781. https://doi.org/10.1016/j.neuroimage.2012.01.021
Fischl, B., Salat, D. H., Busa, E., Albert, M., Dieterich, M., Haselgrove, C., … Dale, A. M. (2002). Whole brain segmentation: Automated labeling of neuroanatomical structures in the human brain. Neuron, 33(3), 341–355. https://doi.org/10.1016/S0896-6273(02)00569-X