All other first.vtks like Thal, Put, etc are built.
OK, that’s interesting; I was under the impression that it was most typically the registration steps in run_first_all that failed, in which case none of the segmentations would be produced.
Firstly, I would confirm that you are able to reproduce the fault by manually executing run_first_all on the relevant T1 image. It may seem like a pointless exercise, but from a software support perspective it makes a very big difference whether MRtrix3 is doing something that is causing an FSL tool to fail, or whether the FSL tool is failing for your data independently of MRtrix3.
The second thing you could try is executing the fsl_anat script. I mentioned here that 5ttgen fsl could conceivably be modified to make use of this FSL-maintained script; it’s possible that some of the extra steps in that script are making the process more robust. (Or maybe I could just duplicate those extra steps)
Interestingly it’s running smoothly on native T1 image. I think the registration was problematic. But a further problem arises: Is it possible to register after 5ttgen?
5ttgen does not incorporate any multi-modal registration, nor does it depend on DWI data in any way.
Update: 5ttgen has finished with this error:
OK, an up-to-date MRtrix3 5ttgen shouldn’t be producing that error. If you run 5ttcheck manually, you should be able to get a more specific error message, and optionally a mask of image voxels where an error was detected.