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

• Published in: PloS one 2022-02, Vol.17 (2), p.e0247343-e0247343
• Main Authors: Beaumont, Jeremy, Gambarota, Giulio, Prior, Marita, Fripp, Jurgen, Reid, Lee B
• Format: Article
• Language: English
• Subjects: 3D printing; Anisotropy; Bioengineering; Biology and Life Sciences; Brain Neoplasms - diagnostic imaging; Case-Control Studies; Cerebrospinal fluid; Cerebrospinal Fluid - diagnostic imaging; Computer Simulation; Connectome - methods; Corruption; Cortex (somatosensory); Data integrity; Data loss; Datasets; Diffusion; Diffusion Tensor Imaging - methods; Epilepsy - diagnostic imaging; Glioma - diagnostic imaging; Gray Matter - diagnostic imaging; Health aspects; Healthy Volunteers; Humans; Image acquisition; Image contrast; Image processing; Image Processing, Computer-Assisted - methods; Image quality; Life Sciences; Magnetic properties; Magnetic resonance; Magnetic resonance imaging; Medical imaging; Medical research; Medicine and Health Sciences; Methods; Neuroimaging; Registration; Research and Analysis Methods; Resonance; Scanners; Scholarships & fellowships; Thalamus; Tissues; White Matter - diagnostic imaging
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0247343

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.