We have very noisy/low SNR structural scans from a sample of children and
adolescents. We are having trouble with skull stripping that is sufficient
for surface-based analysis (e.g. Freesurfer).  A large portion of pial
matter is included along the dorsal and posterior areas of the cortex for
nearly every subject. We have tried multiple options in AFNI skull strip
and FreeSurfer skull strip, with little success.

We have recently tried BET. When adjusting the fractional intensity
threshold to be larger (so more aggressive skull stripping, at 0.6, 0.7,
0.8, ect.), it starts removing parts of the prefrontal cortex, but still
leaves the pial matter.

Are there any additional options that you would recommend trying? when
looking through BET options, none of them jump out at me for addressing
this problem, but maybe I am missing something.


Michelle VanTieghem
PhD student in Psychology
Developmental Affective Neuroscience Lab
Columbia University
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