Hi Jan,
FSL’s FIRST tool is genuinely failing for some of your subjects. Unfortunately 5ttgen fsl is producing an intermediate error regarding one of the internal library functions, rather than providing the error it was intended to (see code here); however fundamentally the issue is that the run_first_all script is failing, and hence 5ttgen fsl cannot proceed.
While I have implemented improvements to the Python library regarding how the outcomes of the run_first_all script are assessed & reported to users, and hope to push this to users, I cannot provide support on the underlying operation of FSL commands themselves. Unless by chance your failure is being caused by unnecessary image down-sampling.
Cheers
Rob