Dear FSL experts,
I am trying to skull strip some baboons and I have some difficulties.
1) Best results are obtained with Bet2 robust brain centre estimation iterative method, Fractional Intensity : ~ 0.20 , threshold gradient : -0.1 and adding the coordinates for centre of initial brain surface sphere. The big baboon skull and the wide layer of muscle are removed however most of the eyes are still there and also cerebellum and brain stem.
Can you give me some advices about FSL BET in baboons ?
2) Plus I have the feeling that histogram of voxel values is changed after BET. When I check the resulting image in mricro, white matter is like in hypersignal and grey matter is a bit missing. Modifying threshold of voxel values to 0 - 255 in mricro enables to see the image in its original contrast, everything is fine but if i try to place this BET resulting image in another software (I tried brainvisa and caret), I have the white matter hypersignal and the missing grey matter.
Can somebody explain to me what's my problem with voxel values after BET ? I guess that this is quite simple, but I don't understand.
Thanks a lot for your help,
Best regards,
Damien
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