TY - CHAP
T1 - Atlas-based brain extraction is robust across rat MRI studies
AU - MacNicol, E.
AU - Ciric, R.
AU - Kim, E.
AU - DiCenso, D.
AU - Cash, D.
AU - Poldrack, R. A.
AU - Esteban, O.
N1 - Funding Information:
Index Terms— brain extraction, preclinical MRI, rodent, MRI, preprocessing Acknowledgments EM is supported by the UK Medical Research Council and King’s College London Doctoral Training Partnership in Biomedical Sciences (MR/N013700/1). OE is supported by the Swiss National Science Foundation, Ambizione grant PZ00P2_185872. This work was supported by the Laura and John Arnold Foundation, the NIH (NBIB R01EB020740), NIMH (R24MH114705 and R24MH117179), the Alzheimer’s Society (AS-PhD-18B-015), and the UK Biotechnology and Biological Sciences Research Council (BB/N009088/1). The authors have no conflicts of interests to disclose.
Publisher Copyright:
© 2021 IEEE.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2021/4/13
Y1 - 2021/4/13
N2 - Brain extraction is a ubiquitous initial step in MRI analysis pipelines. Although there are several solutions for human imaging, existing rodent imaging tools often perform poorly on new data with acquisition protocols and parameters that differ from the images with which the tools were developed. Here, we adapted antsBrainExtraction (from the popular ANTs neuroimaging toolbox), which implements atlasbased brain extraction of adult humans, for use with rat MRI data. The new tool, artsBrainExtraction, was evaluated on 190 images from three different scanners, utilising six imaging protocols that differ in contrast, resolution, and field-of-view. The tool produced highly accurate brain masks in 186 (98%) of the images and adequate masks in the other four. We present a reliable brain extraction tool for rodent images that is agnostic to the imaging protocol and can be extended to further image modalities and non-human populations.
AB - Brain extraction is a ubiquitous initial step in MRI analysis pipelines. Although there are several solutions for human imaging, existing rodent imaging tools often perform poorly on new data with acquisition protocols and parameters that differ from the images with which the tools were developed. Here, we adapted antsBrainExtraction (from the popular ANTs neuroimaging toolbox), which implements atlasbased brain extraction of adult humans, for use with rat MRI data. The new tool, artsBrainExtraction, was evaluated on 190 images from three different scanners, utilising six imaging protocols that differ in contrast, resolution, and field-of-view. The tool produced highly accurate brain masks in 186 (98%) of the images and adequate masks in the other four. We present a reliable brain extraction tool for rodent images that is agnostic to the imaging protocol and can be extended to further image modalities and non-human populations.
KW - Brain extraction
KW - MRI
KW - Preclinical MRI
KW - Preprocessing
KW - Rodent
UR - http://www.scopus.com/inward/record.url?scp=85107212060&partnerID=8YFLogxK
U2 - 10.31219/osf.io/sqxef
DO - 10.31219/osf.io/sqxef
M3 - Conference paper
AN - SCOPUS:85107212060
T3 - Proceedings - International Symposium on Biomedical Imaging
SP - 312
EP - 315
BT - 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021
PB - IEEE Computer Society
T2 - 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021
Y2 - 13 April 2021 through 16 April 2021
ER -