Avoiding data loss: Synthetic MRIs generated from diffusion imaging can replace corrupted structural acquisitions for freesurfer-seeded tractography.

Jeremy Beaumont,Lee B Reid,Giulio Gambarota,Jurgen Fripp,Marita Prior,Dzung Pham

doi:10.1371/journal.pone.0247343

Abstract

Magnetic Resonance Imaging (MRI) motion artefacts frequently complicate structural and diffusion MRI analyses. While diffusion imaging is easily 'scrubbed' of motion affected volumes, the same is not true for T1w or T2w 'structural' images. Structural images are critical to most diffusion-imaging pipelines thus their corruption can lead to disproportionate data loss. To enable diffusion-image processing when structural images are missing or have been corrupted, we propose a means by which synthetic structural images can be generated from diffusion MRI. This technique combines multi-tissue constrained spherical deconvolution, which is central to many existing diffusion analyses, with the Bloch equations that allow simulation of MRI intensities for given scanner parameters and magnetic resonance (MR) tissue properties. We applied this technique to 32 scans, including those acquired on different scanners, with different protocols and with pathology present. The resulting synthetic T1w and T2w images were visually convincing and exhibited similar tissue contrast to acquired structural images. These were also of sufficient quality to drive a Freesurfer-based tractographic analysis. In this analysis, probabilistic tractography connecting the thalamus to the primary sensorimotor cortex was delineated with Freesurfer, using either real or synthetic structural images. Tractography for real and synthetic conditions was largely identical in terms of both voxels encountered (Dice 0.88-0.95) and mean fractional anisotropy (intrasubject absolute difference 0.00-0.02). We provide executables for the proposed technique in the hope that these may aid the community in analysing datasets where structural image corruption is common, such as studies of children or cognitively impaired persons.

Highlights

Synthetic magnetic resonance imaging (MRI) generated from diffusion imaging can replace structural acquisitions for tractography patients’ data from the Hospital dataset was not approved by the Royal Brisbane and Women’s Hospital (RBWH) Human Research Ethics Committee
We demonstrate that by combining these modern methods with MRI simulation based on the use of the Bloch equations [23], synthetic images can be produced that are of sufficient quality to be used in place of genuine structural images in some standard diffusion tractography analyses
The synthetic T1w scans were characterized by a good suppression of the cerebrospinal fluid (CSF) signal and by a high contrast between grey matter, white matter, and CSF, as is typical for MPRAGE acquisitions

Summary

Introduction

Diffusion magnetic resonance imaging (MRI) is a form of medical imaging that can indirectly quantify certain aspects of tissue microstructure related to myelination [e.g. 1], axon density. Synthetic MRIs generated from diffusion imaging can replace structural acquisitions for tractography patients’ data from the Hospital dataset was not approved by the Royal Brisbane and Women’s Hospital (RBWH) Human Research Ethics Committee. The images from the Hospital dataset cannot be shared. For the HCP dataset, the FOD and T1 images (both real and synthetic) are available at https://data.csiro.au/ collection/csiro:53349v2. All numerical results reported in this paper are detailed per subjects in Annexes S1-S5

Methods

Results

Conclusion