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Improved Segmentation of the Intracranial and Ventricular Volumes in Populations with Cerebrovascular Lesions and Atrophy Using 3D CNNs


Successful segmentation of the total intracranial vault (ICV) and ventricles is of critical importance when studying neurodegeneration through neuroimaging. We present iCVMapper and VentMapper, robust algorithms that use a convolutional neural network (CNN) to segment the ICV and ventricles from both single and multi-contrast MRI data. Our models were trained on a large dataset from two multi-site studies (N = 528 subjects for ICV, N = 501 for ventricular segmentation) consisting of older adults with varying degrees of cerebrovascular lesions and atrophy, which pose significant challenges for most segmentation approaches. The models were tested on 238 participants, including subjects with vascular cognitive impairment and high white matter hyperintensity burden. Two of the three test sets came from studies not used in the training dataset. We assessed our algorithms relative to four state-of-the-art ICV extraction methods (MONSTR, BET, Deep Extraction, FreeSurfer, DeepMedic), as well as two ventricular segmentation tools (FreeSurfer, DeepMedic). Our multi-contrast models outperformed other methods across many of the evaluation metrics, with average Dice coefficients of 0.98 and 0.96 for ICV and ventricular segmentation respectively. Both models were also the most time efficient, segmenting the structures in orders of magnitude faster than some of the other available methods. Our networks showed an increased accuracy with the use of a conditional random field (CRF) as a post-processing step. We further validated both segmentation models, highlighting their robustness to images with lower resolution and signal-to-noise ratio, compared to tested techniques. The pipeline and models are available at: and to enable further investigation of the roles of ICV and ventricles in relation to normal aging and neurodegeneration in large multi-site studies.

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We are grateful for the support of the Medical Imaging Trial Network of Canada (MITNEC) Grant #NCT02330510, and the following site Principal investigators: Christian Bocti, Michael Borrie, Howard Chertkow, Richard Frayne, Robin Hsiung, Robert Laforce, Jr., Michael D. Noseworthy, Frank S. Prato, Demetrios J. Sahlas, Eric E. Smith, Vesna Sossi, Alex Thiel, Jean-Paul Soucy, and Jean-Claude Tardif. We are also grateful for the support of the Canadian Atherosclerosis Imaging Network (CAIN) (, and the following investigators: Therese Heinonen, Rob Beanlands, David Spence, Philippe L’Allier, Brian Rutt, Aaron Fenster, Matthias Friedrich, Ben Chow, and Richard Frayne. This research was conducted with the support of the Ontario Brain Institute, an independent non-profit corporation, funded partially by the Ontario government. The opinions, results and conclusions are those of the authors and no endorsement by the Ontario Brain Institute is intended or should be inferred.

Data Accessibility

The developed algorithm and trained models (network weights) are publicly available at: and under the GNU General Public License v3.0. An example dataset is included for testing purposes. We have developed an easy-to-use pipeline with a GUI and thorough documentation for making it accessible to users without programming knowledge. 


This study was funded by the Canadian Institute for Health Research (CIHR) MOP Grant #13129, CIHR Foundation grant #159910, Ontario Brain Institute and the L.C Campbell Foundation. RHS is supported by a Heart and Stroke Clinician-Scientist Phase II Award. The work was also supported by the Medical Imaging Trial Network of Canada (MITNEC) Grant #NCT02330510. Matching funds were provided by participant hospital and research foundations, including the Baycrest Foundation, Bruyere Research Institute, Centre for Addiction and Mental Health Foundation, London Health Sciences Foundation, McMaster University Faculty of Health Sciences, Ottawa Brain and Mind Research Institute, Queen’s University Faculty of Health Sciences, St. Michael’s Hospital, Sunnybrook Health Sciences Centre Foundation, the Thunder Bay Regional Health Sciences Centre, University Health Network, the University of Ottawa Faculty of Medicine, and the Windsor/Essex County ALS Association. The Temerty Family Foundation provided the major infrastructure matching funds.

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Correspondence to Maged Goubran.

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Ntiri, E.E., Holmes, M.F., Forooshani, P.M. et al. Improved Segmentation of the Intracranial and Ventricular Volumes in Populations with Cerebrovascular Lesions and Atrophy Using 3D CNNs. Neuroinform 19, 597–618 (2021).

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  • Total intracranial volume
  • Ventricles
  • Image segmentation
  • Deep learning
  • Vascular lesions
  • Brain atrophy