1. One issue may be the different size head, different topography of the pediatric heads, or different GM/WM values. Also, the bet may be “tuned” to older brain voxel values.
2. I have a set of average MRI templates for pediatric populations. We substitute an age-appropriate MRI template (head, brain, gm/wm priors) for the default FSL brain (usually the MNI 152). I use a modified version of the FSL pipeline (register participant head to template; inverse transform the template brain to participant; expand the transformed brain by 2-3 voxels; mask, then BET). We have pretty much 100% success with this with 7 yr olds. For younger participants (e.g., infants, preschool) or for non-standard participants (e.g., Chinese children), an age-appropriate MRI template is essential.
See http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/
Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015) <http://jerlab.psych.sc.edu/hdeegerp/PWRPublications/abstracts.php?&TablePrimaryKey=410>A database of age-appropriate average MRI templates. Neuroimage, doi:10.1016/j.neuroimage.2015.04.055
And my www site for other references to this.
John
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John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: [log in to unmask] <applewebdata:[log in to unmask]>
HTTP: jerlab.psych.sc.edu
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On 7/1/15, 10:07 AM, "FSL - FMRIB's Software Library on behalf of Rachel Ellenbogen" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Hello,
>
>I am trying to us FSL to do VBM analysis on a population of pediatric (ages 7-17) MRIs. I have been running into a lot of issues with the first BET step. I have tried adjusting the parameters (f, g, c) and have used robust, neck, and eye removal options but haven't had much success, especially in the MRI's for the younger kids. The program often cuts of large portions of the frontal lobe. Has anyone had success with BET/extracting skull from a pediatric population? I am thankful for any suggestions or work arounds!
>
>Thank you!
>
>Rachel
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