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Field of View Normalization in Multi-Site Brain MRI

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Abstract

Multi-site brain MRI analysis is needed in big data neuroimaging studies, but challenging. The challenges lie in almost every analysis step including skull stripping. The diversities in multi-site brain MR images make it difficult to tune parameters specific to subjects or imaging protocols. Alternatively, using constant parameter settings often leads to inaccurate, inconsistent and even failed skull stripping results. One reason is that images scanned at different sites, under different scanners or protocols, and/or by different technicians often have very different fields of view (FOVs). Normalizing FOV is currently done manually or using ad hoc pre-processing steps, which do not always generalize well to multi-site diverse images. In this paper, we show that (a) a generic FOV normalization approach is possible in multi-site diverse images; we show experiments on images acquired from Philips, GE, Siemens scanners, from 1.0T, 1.5T, 3.0T field of strengths, and from subjects 0–90 years of ages; and (b) generic FOV normalization improves skull stripping accuracy and consistency for multiple skull stripping algorithms; we show this effect for 5 skull stripping algorithms including FSL’s BET, AFNI’s 3dSkullStrip, FreeSurfer’s HWA, BrainSuite’s BSE, and MASS. We have released our FOV normalization software at http://www.nitrc.org/projects/normalizefov.

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Acknowledgements

The authors would like to acknowledge Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043 for providing support of the high-performance batch computing environment, Thrasher Research Fund Early Career Award for support to YO, Boston Children’s Hospital and Harvard Medical School Faculty Development Fellowship to YO, NIH R01 EB014947 for support to YO, LZ, KR, PEG, SNM and RLG, NIH R00 HD061485 for support to LZ, NIH K23 CA169021 for support to ERG, and NIH U01 CA154601 and U24 CA180927 for support to YO, XD, ERG and JKC.

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Correspondence to Yangming Ou.

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Jayashree Kalpathy-Cramer and Randy L. Gollub contributed equally.

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Ou, Y., Zöllei, L., Da, X. et al. Field of View Normalization in Multi-Site Brain MRI. Neuroinform 16, 431–444 (2018). https://doi.org/10.1007/s12021-018-9359-z

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