Hi,
I have quantitative T1-data saved as Nifti 16bit integer with scale=1 and intercept=0, intensity range 0-10000.
I convert them to hdr/img and can read them fine into MRIcro or MRIcron.
Now I want to apply brain extraction with BET.
 
It works perfectly as expected when I call BET via the menu entry in MRIcro "Etc" -> Skull strip image ... with fi=0.2
 
But I would like to use the standalone version (bet.exe) via a script. However using bet.exe as
 
bet

-f 0.2
 
produces only 8bit output images with a weird scale. The overall input intensity range 0-10000
is reduced to 256 (obviously 8bit) but this does not suffice since I lose the entire dynamic range
no matter what scaling is applied.
I have tried all sorts of settings using 32bit integer or float inputs etc. nothing works.
When I use BET via menu from MRIcro it preserves the same output data type as the input type
(16 bit integer, 32 bit float whatever).
 
I also tried the new newest version of MRIcro and MRIcron with the accompanying bet.exe
but all the same behaviour.
 
Is there any parameter that forces to maintain the input data type?
 
Any help would be appreciated.