SynthMap: a generative model for synthesis of 3D datasets for quantitative MRI parameter mapping of myelin water fractionDownload PDF

10 Dec 2021, 20:51 (modified: 22 Jun 2022, 18:47)MIDL 2022Readers: Everyone
Keywords: quantitative mri, data synthesis
TL;DR: A generative model for creating large synthetic 3D datasets for training neural networks for quantitative MRI parameter estimation without ground truth, demonstrated on myelin water fraction mapping
Abstract: We present a generative model for synthesis of large scale 3D datasets for quantitative MRI parameter mapping of myelin water fraction (MWF). Training robust neural networks for estimation of quantitative MRI parameters requires large amounts of data. Conventional approaches to tackling data scarcity use spatial augmentations, which may not capture a broad range of possible variations when only a very small initial dataset is available. Furthermore, conventional non linear least squares (NNLS) based methods for MWF estimation are highly sensitive to noise, which means that high quality ground truth MWF parameters are not available for supervised training. Instead of using the noisy NNLS based estimates of MWF parameters from limited real data, we propose to leverage the biophysical model that describes how the MRI signals arise from the underlying tissue parameters to synthetically generate a wide variety of high quality data of the corresponding signals and corresponding parameters for training any CNN based architecture. Our model samples parameter values from a range of naturally occurring prior values for each tissue type. To capture spatial variation, the generative signal decay model is combined with a generative spatial model conditioned on generic tissue segmentations. We demonstrate that our synthetically trained neural network provides superior accuracy over conventional NNLS based methods under the constraints of naturally occuring noise as well as on synthetic low SNR images. Our source code is available at:
Registration: I acknowledge that publication of this at MIDL and in the proceedings requires at least one of the authors to register and present the work during the conference.
Authorship: I confirm that I am the author of this work and that it has not been submitted to another publication before.
Paper Type: both
Primary Subject Area: Application: Radiology
Secondary Subject Area: Image Synthesis
Confidentiality And Author Instructions: I read the call for papers and author instructions. I acknowledge that exceeding the page limit and/or altering the latex template can result in desk rejection.
Code And Data:
5 Replies