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  • In-Vivo Segmentation of the Human Amygdala using Diffusion Tensor Imaging and Probabilistic Tractography

    Final Number:

    Ausaf Bari MD, PhD; Zhong Zheng BS; Antonio DeSalles MD PhD; Nader Pouratian MD, PhD

    Study Design:
    Laboratory Investigation

    Subject Category:

    Meeting: Congress of Neurological Surgeons 2011 Annual Meeting

    Introduction: Animal studies have shown a potential role for deep brain stimulation of the amygdala in the treatment of conditions such as post-traumatic stress disorder, depression and epilepsy. Based on differences in connectivity, subnuclei within the amygdala are likely to play separate functional, pathological, and therapeutic roles. Patient-specific targeting of these subregions poses a challenge for performing DBS of the amygdala in the future . Diffusion tensor imaging-based probabilistic tractography has been used previously to segment other subcortical structures such as the thalamus into functionally distinct regions based on differences in connectivity in a patient-specific manner.

    Methods: MRI T1-weighted anatomical sequences were acquired in a series of 6 healthy volunteers. 20-direction DTI was acquired. Seed masks for the amygdala were generated using FreeSurfer ( and probabilistic diffusion tractography was performed using FSL ( The probability of connection between seed voxels (amygdala) and each voxel in the rest of the brain (including brainstem) was determined and the resulting connectivity matrix was subsequently subjected to k-means clustering analysis with 3 predefined clusters. The resulting segmentation maps were compared to known neuroanatomical organization of the amygdala.

    Results: The amygdala is amenable to in-vivo segmentation into 3 distinct subregions based on its connectivity to the remainder of the brain. The three-dimensional spatial profile of the resulting segments was highly correlated to the known traditional subclassification of the amygdala into basolateral, corticomedial and central nuclear groups.

    Conclusions: DTI-based tractography can be used to derive an in-vivo patient-specific connectivity map of the human amygdala which correlates well with known amygdalar anatomy. This map may be used in the future for pre-operative planning and refinement of DBS targeting within the amygdala.

    Patient Care: This research will advance the exploration of the amygdala as a novel target for deep brian stimulation in the treatment of various challenging mood disorders. In addition, it will advance our knowledge of the neuroanatomy and connectivity of the amygdala and other subcortical limbic structures in living humans.

    Learning Objectives: Role of DBS of the amygdala for mood disorders Probablistic tractography as a tool to segment subcortical structures Neuroanatomy of the amygdala


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