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Dear Sam, This article introduced an automatic way for brain extraction in head CT scan. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446187/ YH 2017-02-16 11:05 GMT+09:00 Matt Glasser <[log in to unmask]>: > That might be quite challenging as BET was probably designed for MRI > images. Another way you can brain extract images is to register them > nonlinearly to a target where you have already defined a brainmask and > then invert the transform and bring the mask back to the individual. > > Peace, > > Matt. > > On 2/15/17, 7:57 PM, "FSL - FMRIB's Software Library on behalf of Sam > Choi" <[log in to unmask] on behalf of [log in to unmask]> wrote: > > >Dear FSLers, > > > >I am working with CT scans of stroke patients and would like to use FSL's > >brain extraction tool (BET) to remove the skull from the brain images. > > > >When I use the BET command (below), the resulting brain image still > >includes the skull and other artifacts. > >bet ct_scan.nii.gz ct_scan_brain.nii.gz > > > >I looked on the FSL forum but did not find much information on CT scans. > >I am wondering if I should experiment with the -f option (fractional > >intensity threshold, between 0-->1) in the BET command until I find an > >appropriate brain outline estimate. For example: > >bet ct_scan.nii.gz ct_scan_brain.nii.gz -f 0.9 > > > >Given that I am working with CT scans of many patients, it is likely the > >-f value will vary for each brain that I am skull stripping, which makes > >this solution quite subjective. I am wondering if there is a more > >'systematic' approach to carry out BET for CT scans (e.g., change voxel > >intensities of the CT scans to create better contrast between skull and > >brain). > > > >Thanks for your help! > > > >Sam >