Hypothalamus and intracranial volume segmentation at the group level by use of a Gradio-CNN framework

This study aimed to develop and evaluate a graphical user interface (GUI) for the automated segmentation of the hypothalamus and intracranial volume (ICV) in brain MRI scans. The interface was designed to facilitate efficient and accurate segmentation for research applications, with a focus on accessibility and ease of use for end-users.

We developed a web-based GUI using the Gradio library integrating deep learning-based segmentation models trained on annotated brain MRI scans. The model utilizes a U-Net architecture to delineate the hypothalamus and ICV. The GUI allows users to upload high-resolution MRI scans, visualize the segmentation results, calculate hypothalamic volume and ICV, and manually correct individual segmentation results. To ensure widespread accessibility, we deployed the interface using ngrok, allowing users to access the tool via a shared link. As an example for the universality of the approach, the tool was applied to a group of 90 patients with Parkinson's disease (PD) and 39 controls.

The GUI demonstrated high usability and efficiency in segmenting the hypothalamus and the ICV, with no significant difference in normalized hypothalamic volume observed between PD patients and controls, consistent with previously published findings. The average processing time per patient volume was 18 s for the hypothalamus and 44 s for the ICV segmentation on a 6 GB NVidia GeForce GTX 1060 GPU. The ngrok-based deployment allowed for seamless access across different devices and operating systems, with an average connection time of less than 5 s.

The developed GUI provides a powerful and accessible tool for applications in neuroimaging. The combination of the intuitive interface, accurate deep learning-based segmentation, and easy deployment via ngrok addresses the need for user-friendly tools in brain MRI analysis. This approach has the potential to streamline workflows in neuroimaging research.