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Validated Automatic Brain Extraction of Head CT Images
NeuroImage (2015)
  • John Muschelli, III, Johns Hopkins University
  • Natalie L Ullman, Johns Hopkins University
  • Daniel F Hanley, Johns Hopkins University
  • Paul Vespa, University of California - Los Angeles
  • Ciprian M Crainiceanu, Johns Hopkins University


X-ray Computed Tomography (CT) imaging of the brain is commonly used in diagnostic settings. Al- though CT scans are primarily used in clinical practice, they are increasingly used in research. A fundamental processing step in brain imaging research is brain extraction – the process of separating the brain tissue from all other tissues. Methods for brain extraction have either been validated but not fully automated, or have been fully automated and informally proposed, but never formally validated.


To systematically analyze and validate the performance of FSL’s brain extraction tool (BET) on head CT images of patients with intracranial hemorrhage. This was done by comparing the manual gold standard with the results of several versions of automatic brain extraction and by estimating the reliability of automated segmentation of longitudinal scans. The effects of the choice of BET parameters and data smoothing is studied and reported.


All images were thresholded using a 0 − 100 Hounsfield units (HU) range. In one variant of the pipeline, data were smoothed using a 3-dimensional Gaussian kernel (σ = 1mm3) and re-thresholded to 0 − 100 HU; in the other, data were not smoothed. BET was applied using 1 of 3 fractional intensity (FI) thresholds: 0.01, 0.1, or 0.35 and any holes in the brain mask were filled.

For validation against a manual segmentation, 36 images from patients with intracranial hemorrhage were selected from 19 different centers from the MISTIE (Minimally Invasive Surgery plus recombinant- tissue plasminogen activator for Intracerebral Evacuation) stroke trial. Intracranial masks of the brain were manually created by one expert CT reader. The resulting brain tissue masks were quantitatively compared to the manual segmentations using sensitivity, specificity, accuracy, and the Dice Similarity Index (DSI). Brain extraction performance across smoothing and FI thresholds was compared using the Wilcoxon signed-rank test.

To estimate the performance in a large number of scans, brain masks were generated from the 6 BET pipelines for 1095 longitudinal scans from 129 patients. The intracranial volume (ICV) of each scan was estimated by multiplying the number of voxels in the brain mask by the dimensions of each voxel for that scan. Failure rates were estimated from visual inspection and an intraclass correlation (ICC) of ICV was estimated using a one-way ANOVA.


Smoothing images improves brain extraction results using BET for all measures except specificity (all p < 0.01, uncorrected), irrespective of the FI threshold. Using an FI of 0.01 or 0.1 performed better than 0.35. Thus, all reported results refer only to smoothed data using an FI of 0.01 or 0.1. Using an FI of 0.01 had a higher median sensitivity (0.9901) than an FI of 0.1 (0.9884, median difference: 0.0014, p < 0.001), accuracy (0.9971 vs. 0.9971; median difference: 0.0001, p < 0.001), and DSI (0.9895 vs. 0.9894; median difference: 0.0004, p < 0.001) and lower specificity (0.9981 vs. 0.9982; median difference: −0.0001, p < 0.001). These measures are all very high indicating that a range of FI values may produce visually indistinguishable brain extractions. Using smoothed data and an FI of 0.01 had a low failure rate (5.2%) and the ICC estimate was high (0.929, 95% CI: 0.91, 0.945) for successfully extracted brains.


BET performs well at brain extraction on thresholded, 1mm3 smoothed CT images with an FI of 0.01 or 0.1. Smoothing before applying BET is an important step not previously discussed in the literature. Analysis code is provided.

  • Segmentation,
  • CT,
  • Neuroimaging
Publication Date
Spring April 7, 2015
Citation Information
John Muschelli, Natalie L Ullman, Daniel F Hanley, Paul Vespa, et al.. "Validated Automatic Brain Extraction of Head CT Images" NeuroImage (2015)
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