Deep learning from MRI-derived labels enables automatic brain tissue classification on human brain CT

Meera Srikrishna, Joana B. Pereira, Rolf A. Heckemann, Giovanni Volpe, Danielle van Westen, Anna Zettergren, Silke Kern, Lars Olof Wahlund, Eric Westman, Ingmar Skoog, Michael Schöll

Research output: Contribution to journalArticlepeer-review


Automatic methods for feature extraction, volumetry, and morphometric analysis in clinical neuroscience typically operate on images obtained with magnetic resonance (MR) imaging equipment. Although CT scans are less expensive to acquire and more widely available than MR scans, their application is currently limited to the visual assessment of brain integrity and the exclusion of co-pathologies. CT has rarely been used for tissue classification because the contrast between grey matter and white matter was considered insufficient. In this study, we propose an automatic method for segmenting grey matter (GM), white matter (WM), cerebrospinal fluid (CSF), and intracranial volume (ICV) from head CT images. A U-Net deep learning model was trained and validated on CT images with MRI-derived segmentation labels. We used data from 744 participants of the Gothenburg H70 Birth Cohort Studies for whom CT and T1-weighted MR images had been acquired on the same day. Our proposed model predicted brain tissue classes accurately from unseen CT images (Dice coefficients of 0.79, 0.82, 0.75, 0.93 and 0.98 for GM, WM, CSF, brain volume and ICV, respectively). To contextualize these results, we generated benchmarks based on established MR-based methods and intentional image degradation. Our findings demonstrate that CT-derived segmentations can be used to delineate and quantify brain tissues, opening new possibilities for the use of CT in clinical practice and research.

Original languageEnglish
Article number118606
Publication statusPublished - 2021 Dec

Subject classification (UKÄ)

  • Radiology, Nuclear Medicine and Medical Imaging

Free keywords

  • Brain image segmentation
  • computed tomography (CT)
  • Convolutional neural networks (CNN)
  • Deep learning


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