7T MRI subthalamic nucleus atlas for use with 3T MRI

Abstract

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces motor symptoms in most patients with Parkinson disease (PD), yet may produce untoward effects. Investigation of DBS effects requires accurate localization of the STN, which can be difficult to identify on magnetic resonance images collected with clinically available 3T scanners. The goal of this study is to develop a high-quality STN atlas that can be applied to standard 3T images. We created a high-definition STN atlas derived from seven older participants imaged at 7T. This atlas was nonlinearly registered to a standard template representing 56 patients with PD imaged at 3T. This process required development of methodology for nonlinear multimodal image registration. We demonstrate mm-scale STN localization accuracy by comparison of our 3T atlas with a publicly available 7T atlas. We also demonstrate less agreement with an earlier histological atlas. STN localization error in the 56 patients imaged at 3T was less than 1 mm on average. Our methodology enables accurate STN localization in individuals imaged at 3T. The STN atlas and underlying 3T average template in MNI space are freely available to the research community. The image registration methodology developed in the course of this work may be generally applicable to other datasets.

Keywords: Parkinson disease; atlas; deep brain stimulation; image registration; subthalamic nucleus.

Fig. 1

Registration schemes used in average template creation. Arrows indicate information flow; image stacks represent iteration over all individuals in a given cohort. (a) Creating T1- and T2-weighted average templates. Both SU and WU templates were created according to this scheme. (b) Identifying WU participant for the registration target for refined WU templates. Orange indicates WU data, green indicates SU data.

Fig. 2

Creation of SU_7T_T2w_T template. (a) Triplanar view of registration target (SU_7T_T2w_t). (b) Averaged SU_7T_T2w_T template. Both images are in 7T data space. From left to right: coronal, axial, and sagittal (right hemisphere). Note well-matched anatomical detail achieved by bm-cmg and improved contrast to noise ratio. The cross-hair is centered on the right STN.

Fig. 3

Interrater agreement between raters R1, R2, and R3, delineating the STN in seven SU_7T_T2w images. The error bars denote ±2.7 standard deviations. Red “+” are outliers.

Fig. 4

Probabilistic representation of the STN in SU data space. From left to right: coronal, axial, sagittal (right hemisphere), and sagittal (left hemisphere).

Fig. 5

(a) WU_3T_T2w_T averaged template. (b) SU_7T_T2w_T averaged template. From left to right: sagittal, coronal, and axial plane views. The red outlines are edge maps computed by FSL Slicer tool on the WU 3T template and duplicated on the SU 7T template. Note good match achieved by bm-cmg (whole-brain averaged alignment error = 1.3 mm).

Fig. 6

Subcortical structures in WU data space. The following structures were delineated in SU space and resampled in WU space: STN (yellow) and RN (red). For comparison, RN was directly delineated on the WU_3T_T2_T template (green). (a) WU_3T_T2_T template; (b) SU_7T_T2_T template resampled in WU space. From left to right: axial, coronal, sagittal (right hemisphere), and sagittal (left hemisphere).

Fig. 7

(a) WU 3T and (b) SU 7T T2-weighted templates in MNI152 space. MNI152 plane coordinates are shown under each slice. Edge maps (red contours) were defined on the 3T template and duplicated on the 7T template.

Fig. 8

Subcortical structures in MNI152 space. From left to right: coronal, axial, sagittal (right hemisphere), and sagittal (left hemisphere). MNI152 plane coordinates are shown under each slice. Green: STN originally delineated on the SU_7T_T2w_T template; blue: RN originally delineated on the SU_7T_T2w_T template; red: RN originally delineated on the WU_3T_T2w_T template.

Fig. 9

Volume-matched STN boundaries defined in three atlases and represented in MNI152 space. The underlay is the WU_3T_T2w_T template in MNI152 space. Green: histologic atlas (Mai); yellow: current result; red: previously published 7T atlas (Wang). MNI152 plane coordinates are shown for each row. From left to right: coronal, axial, and sagittal (right hemisphere).