Structural Magnetic Resonance Imaging (MRI) is widely used in neuroimaging research and clinical practice, but structural MRI volumes may retain facial and cranial anatomical information that raises privacy concerns. Existing deep learning-based brain extraction methods generally produce a single fixed output, limiting flexibility when different applications require different balances between privacy and anatomical preservation. This paper presents a configurable privacy-preserving MRI processing workflow that extends deep learning-based brain extraction through adaptive anatomical preservation, interactive preservation selection, and integrated quality control. The workflow employs SynthStrip for automated brain extraction, followed by morphological mask expansion to generate configurable shell-based preservation levels. An Interactive Preservation Framework enables users to compare preservation configurations and select an appropriate output, while an integrated Quality Control Framework provides multi-plane visualisation and brain-mask overlay verification. The workflow was implemented in Python using open-source neuroimaging libraries within the Renku reproducible research environment and evaluated using structural T1-weighted MRI data from the publicly available IXI dataset. Experimental results demonstrate anatomically plausible brain extraction and configurable preservation outputs, supported by systematic visual verification. The principal contribution is a modular and reproducible MRI preprocessing framework that enhances deep learning-based brain extraction with configurable anatomical preservation, interactive user-guided processing, and integrated quality control. The workflow provides a practical foundation for privacy-oriented neuroimaging research and collaborative medical image analysis.

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