Hi all,
I've been having the same problem, namely that the alternative_mask option
at the bottom of the design file never actually takes effect. I tried two
things: I ran a full first level analysis by specifying an alternative mask
in the fsf file, while 1) leaving the BET option turned on and 2)
de-activating the BET option in the Pre-Stats (just in case the two things
somehow conflict).
Unfortunately, the alternative mask was never used. As was mention in the
previous post, I would expect the mask file to be identical to the one
requested in the design file. Instead, from what I can see from the log file
fSL ignores this option and uses either betting or regular thresholding to
generate the mask depending on whether BET is on or off.
I've read this thread very carefully but it still seems rather inconclusive
as to what the solution to this problem really is and whether the
alternative_mask option really works or not.
Any help would be greatly appreaciated.
Thanks
Marios
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