I try to do run_first_all on T1 images that are already extracted from the
skull. flirt_first fails, but it does work when I call it separately using
the -b option. However, then I have to manually call the rest of the
run_first_all batch; is there a quicker way of doing this? (Can one, e.g.
set options for the flirt_first routine when using run_first_all?).
NB I noticed that information on the fsl homepage regarding run_first_all is
different from what the command line says.
Many thanks
Dom
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