Multi-atlas image registration of clinical data with automated quality assessment using ventricle segmentation
Research output: Contribution to journal › Journal article › Research › peer-review
Standard
Multi-atlas image registration of clinical data with automated quality assessment using ventricle segmentation. / Dubost, Florian; Bruijne, Marleen de; Nardin, Marco; Dalca, Adrian V; Donahue, Kathleen L; Giese, Anne-Katrin; Etherton, Mark R; Wu, Ona; Groot, Marius de; Niessen, Wiro; Vernooij, Meike; Rost, Natalia S; Schirmer, Markus D.
In: Medical Image Analysis, Vol. 63, 101698, 2020.Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Multi-atlas image registration of clinical data with automated quality assessment using ventricle segmentation
AU - Dubost, Florian
AU - Bruijne, Marleen de
AU - Nardin, Marco
AU - Dalca, Adrian V
AU - Donahue, Kathleen L
AU - Giese, Anne-Katrin
AU - Etherton, Mark R
AU - Wu, Ona
AU - Groot, Marius de
AU - Niessen, Wiro
AU - Vernooij, Meike
AU - Rost, Natalia S
AU - Schirmer, Markus D
N1 - Copyright © 2020 Elsevier B.V. All rights reserved.
PY - 2020
Y1 - 2020
N2 - Registration is a core component of many imaging pipelines. In case of clinical scans, with lower resolution and sometimes substantial motion artifacts, registration can produce poor results. Visual assessment of registration quality in large clinical datasets is inefficient. In this work, we propose to automatically assess the quality of registration to an atlas in clinical FLAIR MRI scans of the brain. The method consists of automatically segmenting the ventricles of a given scan using a neural network, and comparing the segmentation to the atlas ventricles propagated to image space. We used the proposed method to improve clinical image registration to a general atlas by computing multiple registrations - one directly to the general atlas and others via different age-specific atlases - and then selecting the registration that yielded the highest ventricle overlap. Finally, as an example application of the complete pipeline, a voxelwise map of white matter hyperintensity burden was computed using only the scans with registration quality above a predefined threshold. Methods were evaluated in a single-site dataset of more than 1000 scans, as well as a multi-center dataset comprising 142 clinical scans from 12 sites. The automated ventricle segmentation reached a Dice coefficient with manual annotations of 0.89 in the single-site dataset, and 0.83 in the multi-center dataset. Registration via age-specific atlases could improve ventricle overlap compared to a direct registration to the general atlas (Dice similarity coefficient increase up to 0.15). Experiments also showed that selecting scans with the registration quality assessment method could improve the quality of average maps of white matter hyperintensity burden, instead of using all scans for the computation of the white matter hyperintensity map. In this work, we demonstrated the utility of an automated tool for assessing image registration quality in clinical scans. This image quality assessment step could ultimately assist in the translation of automated neuroimaging pipelines to the clinic.
AB - Registration is a core component of many imaging pipelines. In case of clinical scans, with lower resolution and sometimes substantial motion artifacts, registration can produce poor results. Visual assessment of registration quality in large clinical datasets is inefficient. In this work, we propose to automatically assess the quality of registration to an atlas in clinical FLAIR MRI scans of the brain. The method consists of automatically segmenting the ventricles of a given scan using a neural network, and comparing the segmentation to the atlas ventricles propagated to image space. We used the proposed method to improve clinical image registration to a general atlas by computing multiple registrations - one directly to the general atlas and others via different age-specific atlases - and then selecting the registration that yielded the highest ventricle overlap. Finally, as an example application of the complete pipeline, a voxelwise map of white matter hyperintensity burden was computed using only the scans with registration quality above a predefined threshold. Methods were evaluated in a single-site dataset of more than 1000 scans, as well as a multi-center dataset comprising 142 clinical scans from 12 sites. The automated ventricle segmentation reached a Dice coefficient with manual annotations of 0.89 in the single-site dataset, and 0.83 in the multi-center dataset. Registration via age-specific atlases could improve ventricle overlap compared to a direct registration to the general atlas (Dice similarity coefficient increase up to 0.15). Experiments also showed that selecting scans with the registration quality assessment method could improve the quality of average maps of white matter hyperintensity burden, instead of using all scans for the computation of the white matter hyperintensity map. In this work, we demonstrated the utility of an automated tool for assessing image registration quality in clinical scans. This image quality assessment step could ultimately assist in the translation of automated neuroimaging pipelines to the clinic.
U2 - 10.1016/j.media.2020.101698
DO - 10.1016/j.media.2020.101698
M3 - Journal article
C2 - 32339896
VL - 63
JO - Medical Image Analysis
JF - Medical Image Analysis
SN - 1361-8415
M1 - 101698
ER -
ID: 240735749