Objective: This work is motivated by the need for atlas creation tools for susceptibility maps presurgically acquired for deep brain stimulation (DBS). Segmentations aid in electrode targeting and longitudinal analysis in DBS candidates. Susceptibility maps provide excellent contrast of targets, including the subthalamic nucleus (STN), globus pallidus internus and externus (GP), substantia nigra (SN), dentate nucleus (DN) and putamen (PUT). A multi-contrast atlas creation tool improving target visualization is presented, with scripts available upon publication.

Background: Quantitative susceptibility maps (QSMs) have demonstrated superior contrast^1-3 on deep gray nuclei targeted in DBS. Pathological changes result in poor registration to healthy subjects atlases⁴ and require atlases such as McGill PD-25^5,6. Study-specific atlases account for pathology and best represent populations of interest⁷. Hybrid templates T1w and QSM atlases exist^8,9 but increase registration error. Existing toolboxes^12,13 contain repositories¹⁴ rather than atlas creation tools. Source separation and myelin mapping further improve target contrasts and are included.

Method: QSMs acquired from a multi-echo gradient echo sequence and susceptibility^{15,16,17,18,19,20,21} and R2*²², source separation²³ and myelin maps²⁴ were reconstructed. The magnitude T2*w atlas was generated after bias correction²⁵, brain extraction²⁶, and template construction²⁷ in Advanced Normalization Tools²⁸ with co-registered susceptibility and relaxation atlases. Inverse transforms map segmentations to patient space [figure1].

Results: The proposed atlas shows improvement over the McGill atlas in segmentations [figure2]. Applying transforms to relaxation and susceptibility map generates atlases in [fgure3]. The DN visualization, STN/SN delineation and GP/PUT contrast is improved in the susceptibility maps χ, χ+ [figure4] compared to structural T1w. White matter tracts on negative source χ– and myelin fraction v are visible [figure5].

Conclusion: The proposed tool creates high contrast atlases of DBS targets and myelin mapping improves depiction of white matter tracts, critical trajectory planning. The added contrasts are reconstructed the presurgical QSM sequence. Other targets including ventral intermediate, centromedian, and the anterior thalamic nuclei can be explored. Output segmentations aid in surgical outcome prediction^29,30 from preoperative imaging.

Created template to patient space.

Masks via McGill atlas and proposed method.

Presented multi-contrast atlas.

White matter tracts on mGRE maps.

Improved visualization GP, PUT, STN, SN, and DN.

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24. Şişman M, Nguyen TD, Roberts AG, et al. Microstructure-Informed Myelin Mapping (MIMM) from Gradient Echo MRI using Stochastic Matching Pursuit. Cold Spring Harbor Laboratory; 2023.
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