MPRAGElike: A novel approach to generate T1w images from multi-contrast gradient echo images for brain segmentation

Abstract

Purpose

Brain segmentation and multi-parameter mapping (MPM) are important steps in neurodegenerative disease characterization. However, acquiring both a high-resolution T1w sequence like MPRAGE (standard input to brain segmentation) and an MPM in the same neuroimaging protocol increases scan time and patient discomfort, making it difficult to combine both in clinical examinations.

Methods

A novel approach to synthesize T1w images from MPM images, named MPRAGE_like, is proposed and compared to the standard technique used to produce synthetic MPRAGE images (synMPRAGE). Twenty-three healthy subjects were scanned with the same imaging protocol at three different 7T sites using universal parallel transmit RF pulses. SNR, CNR, and automatic brain segmentation results from both MPRAGE_like and synMPRAGE were compared against an acquired MPRAGE.

Results

The proposed MPRAGE_like technique produced higher SNR values than synMPRAGE for all regions evaluated while also having higher CNR values for subcortical structures. MPRAGE was still the image with the highest SNR values overall. For automatic brain segmentation, MPRAGE_like outperformed synMPRAGE when compared to MPRAGE (median Dice Similarity Coefficient of 0.90 versus 0.29 and Average Asymmetric Surface Distance of 0.33 versus 2.93 mm, respectively), in addition to being simple, flexible, and considerably more robust to low image quality than synMPRAGE.

Conclusion

The MPRAGE_like technique can provide a better and more reliable alternative to synMPRAGE as a substitute for MPRAGE, especially when automatic brain segmentation is of interest and scan time is limited.