nikhil deveshwar

EECS Department, University of California, Berkeley

Technical Report No. UCB/EECS-2023-225

August 11, 2023

http://www2.eecs.berkeley.edu/Pubs/TechRpts/2023/EECS-2023-225.pdf

Despite the proliferation of deep learning techniques for accelerated MRI acquisition and enhanced image reconstruction, construction of large and diverse MRI datasets continues to pose a barrier for effective clinical translation of these technologies. One major challenge is in collecting the MRI raw data (required for image reconstruction) from clinical scanning, as only magnitude images are typically saved and used for clinical assessment and diagnosis. The image phase and multi-channel RF coil information are not retained when magnitude-only images are saved in clinical imaging archives. Additionally, preprocessing used for data in clinical imaging can lead to biased results. While several groups have begun concerted efforts to collect large amounts of MRI raw data, current databases are limited in the diversity of anatomy, pathology, annotations, and acquisition types they contain. To address this, we present a method for synthesizing realistic MR data from magnitude-only data, allowing for the use of diverse data from clinical imaging archives in advanced MRI reconstruction development. Our method uses a conditional GAN based framework to generate synthetic phase images from input magnitude images. We then apply ESPIRiT to derive RF coil sensitivity maps from fully sampled real data to generate multi-coil data. The synthetic data generation method was evaluated by comparing image reconstruction results from training Variational Networks either with real data or synthetic data. We demonstrate that the Variational Network trained on synthetic MRI data from our method, consisting of GAN-derived synthetic phase and multi-coil information, outperformed Variational Networks trained on data with synthetic phase generated using current state of the art methods. Additionally, we demonstrate that the variational networks trained with synthetic k-space data from our method perform comparably to image reconstruction networks trained on undersampled real k-space data.

Advisors: Michael Lustig

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BibTeX citation:

@mastersthesis{deveshwar:EECS-2023-225,
    Author= {deveshwar, nikhil},
    Title= {Synthesizing Complex-Valued MRI data from Magnitude-Only Images},
    School= {EECS Department, University of California, Berkeley},
    Year= {2023},
    Month= {Aug},
    Url= {http://www2.eecs.berkeley.edu/Pubs/TechRpts/2023/EECS-2023-225.html},
    Number= {UCB/EECS-2023-225},
    Abstract= {Despite the proliferation of deep learning techniques for accelerated MRI acquisition and enhanced image reconstruction, construction of large and diverse MRI datasets continues to pose a barrier for effective clinical translation of these technologies. One major challenge is in collecting the MRI raw data (required for image reconstruction) from clinical scanning, as only magnitude images are typically saved and used for clinical assessment and diagnosis.  The image phase and multi-channel RF coil information are not retained when magnitude-only images are saved in clinical imaging archives. Additionally, preprocessing used for data in clinical imaging can lead to biased results. While several groups have begun concerted efforts to collect large amounts of MRI raw data, current databases are limited in the diversity of anatomy, pathology, annotations, and acquisition types they contain. To address this, we present a method for synthesizing realistic MR data from magnitude-only data, allowing for the use of diverse data from clinical imaging archives in advanced MRI reconstruction development. Our method uses a conditional GAN based framework to generate synthetic phase images from input magnitude images. We then apply ESPIRiT to derive RF coil sensitivity maps from fully sampled real data to generate multi-coil data. The synthetic data generation method was evaluated by comparing image reconstruction results from training Variational Networks either with real data or synthetic data. We demonstrate that the Variational Network trained on synthetic MRI data from our method, consisting of GAN-derived synthetic phase and multi-coil information, outperformed Variational Networks trained on data with synthetic phase generated using current state of the art methods. Additionally, we demonstrate that the variational networks trained with synthetic k-space data from our method perform comparably to image reconstruction networks trained on undersampled real k-space data.},
}

EndNote citation:

%0 Thesis
%A deveshwar, nikhil 
%T Synthesizing Complex-Valued MRI data from Magnitude-Only Images
%I EECS Department, University of California, Berkeley
%D 2023
%8 August 11
%@ UCB/EECS-2023-225
%U http://www2.eecs.berkeley.edu/Pubs/TechRpts/2023/EECS-2023-225.html
%F deveshwar:EECS-2023-225