DeepFLAIR: A neural network approach to mitigate signal and contrast loss in temporal lobes at 7 Tesla FLAIR images

• Published in: Magnetic resonance imaging Vol. 110; pp. 57 - 68
• Main Authors: Uher, Daniel, Drenthen, Gerhard S., Poser, Benedikt A., Hofman, Paul A.M., Wagner, Louis G., van Lanen, Rick H.G.J., Hoeberigs, Christianne M., Colon, Albert J., Schijns, Olaf E.M.G., Jansen, Jacobus F.A., Backes, Walter H.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01-07-2024
• Subjects: Artifact removal; FLAIR; Machine learning; Ultra-high field MRI; Artifact removal; FLAIR; Ultra-high field MRI; Machine learning
• ISSN: 0730-725X; 1873-5894
• DOI: 10.1016/j.mri.2024.04.013

Higher magnetic field strength introduces stronger magnetic field inhomogeneities in the brain, especially within temporal lobes, leading to image artifacts. Particularly, T2-weighted fluid-attenuated inversion recovery (FLAIR) images can be affected by these artifacts. Here, we aimed to improve the FLAIR image quality in temporal lobe regions through image processing of multiple contrast images via machine learning using a neural network.
Thirteen drug-resistant MR-negative epilepsy patients (age 29.2 ± 9.4y, 5 females) were scanned on a 7 T MRI scanner. Magnetization-prepared (MP2RAGE) and saturation-prepared with 2 rapid gradient echoes, multi-echo gradient echo with four echo times, and the FLAIR sequence were acquired. A voxel-wise neural network was trained on extratemporal-lobe voxels from the acquired structural scans to generate a new FLAIR-like image (i.e., deepFLAIR) with reduced temporal lobe inhomogeneities. The deepFLAIR was evaluated in temporal lobes through signal-to-noise (SNR), contrast-to-noise (CNR) ratio, the sharpness of the gray-white matter boundary and joint-histogram analysis. Saliency mapping demonstrated the importance of each input image per voxel.
SNR and CNR in both gray and white matter were significantly increased (p < 0.05) in the deepFLAIR's temporal ROIs, compared to the FLAIR. The gray-white matter boundary sharpness was either preserved or improved in 10/13 right-sided temporal regions and was found significantly increased in the ROIs. Multiple image contrasts were influential for the deepFLAIR reconstruction with the MP2RAGE second inversion image being the most important.
The deepFLAIR network showed promise to restore the FLAIR signal and reduce contrast attenuation in temporal lobe areas. This may yield a valuable tool, especially when artifact-free FLAIR images are not available.
•7 T FLAIR often suffers from signal dropout in temporal lobes.•A subject-specific neural network to reduce the artifacts in post-processing.•The network reconstructs per voxel the FLAIR signal from other structural scans.•Improved SNR and CNR were observed in the attenuated regions.•Further developments may yield deepFLAIR a helpful tool to combat signal dropout.