Jan / anybody else who has had issues with
5ttgen fsl or
labelsgmfix (I know there’s plenty of you out there),
I’ve now merged an update to the MRtrix3 master branch that alters how these scripts assess the outcomes of the FSL
run_first_all script and report any issues back to the user. It should also negate the necessity to disable SGE. While it can’t prevent overall failure of the script if FIRST is genuinely unable to segment one or more structures, I’m hoping that this new solution will be more robust and provide more meaningful feedback. So any independent testing of these changes with problematic data would be very much appreciated.
Note that updating MRtrix3 via the master branch will not alter the outcome of any command, unless the existing outcome is considered egregious. Any changes to MRtrix3 that alter outcomes that may otherwise be considered reasonable are reserved for a tagged update, with associated announcement about those changes. Therefore, updating MRtrix3 on the
master branch can be done without fear of altering experimental outcomes.