CG-SENSE revisited: Results from the first ISMRM reproducibility challenge

PURPOSE

The aim of this work is to shed light on the issue of reproducibility in MR image reconstruction in the context of a challenge. Participants had to recreate the results of "Advances in sensitivity encoding with arbitrary k-space trajectories" by Pruessmann et al. METHODS: The task of the challenge was to reconstruct radially acquired multicoil k-space data (brain/heart) following the method in the original paper, reproducing its key figures. Results were compared to consolidated reference implementations created after the challenge, accounting for the two most common programming languages used in the submissions (Matlab/Python).

RESULTS

Visually, differences between submissions were small. Pixel-wise differences originated from image orientation, assumed field-of-view, or resolution. The reference implementations were in good agreement, both visually and in terms of image similarity metrics.

DISCUSSION AND CONCLUSION

While the description level of the published algorithm enabled participants to reproduce CG-SENSE in general, details of the implementation varied, for example, density compensation or Tikhonov regularization. Implicit assumptions about the data lead to further differences, emphasizing the importance of sufficient metadata accompanying open datasets. Defining reproducibility quantitatively turned out to be nontrivial for this image reconstruction challenge, in the absence of ground-truth results. Typical similarity measures like NMSE of SSIM were misled by image intensity scaling and outlier pixels. Thus, to facilitate reproducibility, researchers are encouraged to publish code and data alongside the original paper. Future methodological papers on MR image reconstruction might benefit from the consolidated reference implementations of CG-SENSE presented here, as a benchmark for methods comparison.

Transfer learning in deep neural network based under-sampled MR image reconstruction

In Magnetic Resonance Imaging (MRI), the success of deep learning-based under-sampled MR image reconstruction depends on: (i) size of the training dataset, (ii) generalization capabilities of the trained neural network. Whenever there is a mismatch between the training and testing data, there is a need to retrain the neural network from scratch with thousands of MR images obtained using the same protocol. This may not be possible in MRI as it is costly and time consuming to acquire data. In this research, a transfer learning approach i.e. end-to-end fine tuning is proposed for U-Net to address the data scarcity and generalization problems of deep learning-based MR image reconstruction. First the generalization capabilities of a pre-trained U-Net (initially trained on the human brain images of 1.5 T scanner) are assessed for: (a) MR images acquired from MRI scanners of different magnetic field strengths, (b) MR images of different anatomies and (c) MR images under-sampled by different acceleration factors. Later, end-to-end fine tuning of the pre-trained U-Net is proposed for the reconstruction of the above-mentioned MR images (i.e. (a), (b) and (c)). The results show successful reconstructions obtained from the proposed method as reflected by the Structural SIMilarity index, Root Mean Square Error, Peak Signal-to-Noise Ratio and central line profile of the reconstructed images.