Hi Wolf,
I always run things from the command line but never managed to get it to go
this far. Which version of fSL are you using? I have the latest version
installed on my machine.
Perhaps I misinterpreted what the alternative mask option does, but it would
seem from the log info you sent that it merely masks the filtered data, then
uses regular thresholding (consistent with BET being turned off) to generate
a mask anyway. I thought that what one enters as an alternative mask is the
actual mask used for the main stats but the info you sent does not seem to
support that.
Thanks
Marios
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