DBSegment: Fast and robust segmentation of deep brain structures considering domain generalisation

in Human Brain Mapping (2022)

Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by ... [more ▼]

Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by-registration approach, where subject magnetic resonance imaging (MRIs) are mapped to a template with well-defined segmentations. However, registration-based pipelines are time-consuming, thus, limiting their clinical use. This paper uses deep learning to provide a one-step, robust, and efficient deep brain segmentation solution directly in the native space. The method consists of a preprocessing step to conform all MRI images to the same orientation, followed by a convolutional neural network using the nnU-Net framework. We use a total of 14 datasets from both research and clinical collections. Of these, seven were used for training and validation and seven were retained for testing. We trained the network to segment 30 deep brain structures, as well as a brain mask, using labels generated from a registration-based approach. We evaluated the generalizability of the network by performing a leave-one-dataset-out cross-validation, and independent testing on unseen datasets. Furthermore, we assessed cross-domain transportability by evaluating the results separately on different domains. We achieved an average dice score similarity of 0.89 ± 0.04 on the test datasets when compared to the registration-based gold standard. On our test system, the computation time decreased from 43 min for a reference registration-based pipeline to 1.3 min. Our proposed method is fast, robust, and generalizes with high reliability. It can be extended to the segmentation of other brain structures. It is publicly available on GitHub, and as a pip package for convenient usage. [less ▲]

Initialisation of Deep Brain Stimulation Parameters with Multi-objective Optimisation Using Imaging Data

in Bildverarbeitung für die Medizin 2022 (2022)

Following the deep brain stimulation (DBS) surgery, the stimulation parameters are manually tuned to reduce symptoms. This procedure can be timeconsuming, especially with directional leads. We propose an ... [more ▼]

Following the deep brain stimulation (DBS) surgery, the stimulation parameters are manually tuned to reduce symptoms. This procedure can be timeconsuming, especially with directional leads. We propose an automated methodology to initialise contact configurations using imaging techniques. The goal is to maximise the electric field on the target while minimising the spillover, and the electric field on regions of avoidance. By superposing pre-computed electric fields, we solve the optimisation problem in less than a minute, much more efficient compared to finite element methods. Our method offers a robust and rapid solution, and it is expected to considerably reduce the time required for manual parameter tuning. [less ▲]

Impressive weight gain after deep brain stimulation of nucleus accumbens in treatment- ­ resistant bulimic anorexia nervosa

in BMJ Case Reports (2020)

Anorexia nervosa (AN) severely impacts individual’s mental and physical health as well as quality of life. In 21% of cases no durable response to conservative treatment can be obtained. The serious course ... [more ▼]

Anorexia nervosa (AN) severely impacts individual’s mental and physical health as well as quality of life. In 21% of cases no durable response to conservative treatment can be obtained. The serious course of the disease in the most severely affected patients justifies invasive treatment options. One of the treatment methods increasingly used in recent years is deep brain stimulation (DBS). A 42-year- old woman suffering from chronic AN of the bulimic subtype shows a 46.9% weight gain and a subjective increase in quality of life, 12 months after bilateral nucleus accumbens (NAcc) DBS implantation. No improvement in comorbid depression could be achieved. DBS of the NAcc is a treatment option to be considered in severe AN when conventional treatment modalities recommended by evidence-based guidelines have not been able to bring lasting relief to the patient’s suffering. [less ▲]