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Abstract #2134

Thresholding to remove fluid from FreeSurfer segmentations of quantitative brain maps – a simple solution to a painful problem

Simran Kukran1,2, Joely Smith 1,3, Ben Statton4, Luke Dixon3,5, Stefanie Thust6,7,8, Iulius Dragonu9, Sarah Cardona3, Mary Finnegan3, Rebecca Quest1,3, Neal Bangerter1,10, Dow Mu Koh2, Peter Lally1, Matthew Orton2, and Matthew Grech Sollars11,12
1Bioengineering, Imperial College London, London, United Kingdom, 2Radiotherapy and Imaging, Institute of Cancer Research, London, United Kingdom, 3Department of Imaging, Imperial College Healthcare NHS Trust, London, United Kingdom, 4London Institute of Medical Sciences, Medical Research Council, London, United Kingdom, 5Surgery and Cancer, Imperial College London, London, United Kingdom, 6Precision Imaging Beacon, School of Medicine, University of Nottingham, Nottingham, United Kingdom, 7School of Physics and Astronomy, University of Nottingham, Nottingham, United Kingdom, 8Dept. of Brian Rehabilitation and Repair, UCL Institute of Neurology, London, United Kingdom, 9Research and Collaborations UK, Siemens Healthcare Ltd, Camberley, United Kingdom, 10Computer and Electrical Engineering, Boise State University, Boise, ID, United States, 11Centre for Medical Imaging and Computing, UCL, London, United Kingdom, 12University College London Hospitals NHS Foundation Trust, London, United Kingdom

Synopsis

Keywords: Segmentation, MR Fingerprinting

Motivation: Segmentation of quantitative maps is required to compute anatomical region mean relaxation times. FreeSurfer is designed to automatically segment conventional weighted images. Voxels of CSF contaminate tissue segmentations in some healthy volunteers, skewing the mean T1 or T2.

Goal(s): To remove contaminant fluid from tissue regions of interest in T1 and T2 maps.

Approach: Mean T1 or T2 of CSF in ventricles is used as a maximum threshold within brain tissue.

Results: Thresholding prior to 2D erosion of masks removes contaminant CSF and prevents erroneous variation between 10 healthy volunteers.

Impact: A simple threshold-based correction of FreeSurfer segmentation applied to quantitative T1 and T2 maps. The same threshold can be applied to all subjects in one step, eliminating the need for laborious manual adjustment.

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Abstract

Keywords