Unable to specify -tempdir flag in dwifslpreproc

Hello experts, it’s been a while but I’m back and analyzing more data. The folks who manage our HPC resources set me up with a new shiny version of MRtrix3, and I am at the stage where I’m running dwifslpreproc. Unlike with dwipreproc, I am unable to specify where I want the -tempdir to be and unable to name it. Since eddy_cuda and eddy_openmp tend to throw errors in my HPC setup, being able to tag -tempdir with the subject ID has been extremely useful for debugging, and I even sometimes have success running eddy from within the tempdir directories (where running within the overall dwipreproc/dwifslpreproc command fails). I can’t find any new flags in the dwifslpreproc -help to set -tempdir, am I missing something?

Thanks in advance for any advice! -Rachael

Looking at the relevant docs (you’re essentially running our dev branch…), I think this option is now called -scratch

By the way, if by ‘shiny new version’, you mean 3.0_RC4, please note that it wasn’t intended for release, as stated on the corresponding GitHub release note – see discussion and full mea culpa on this thread.

Oh wow, okay-- the price of my being out of the loop. (I did think it was strange that I had to go and hunt in the /bin directory to figure out why dwipreproc didn’t work.) Thank you for this info, I’ll pass it along to our sysadmins.

@jdtournier: I wonder if we now have more people using dev than master:grimacing: