dwipreproc : temporary folders ( nooutput)

1

Hello experts,
I am super new to MRtrix . I am pre-processing some data for my pre-clinical research. So i am performing dwipreproc

i have used the following algorithm

module load mrtrix/3.0_rc_latest 
module load fsl

dwi_directory=$1
dwi_file=${dwi_directory}/dwi_dn_dg_convertedfromnii.mif
dwi_file2=${dwi_directory}/dwi_dn_dg_contecated.mif
dwifslpreproc ${dwi_file} ${dwi_file/.mif/}_prdone.mif -rpe_none -pe_dir AP -se_epi ${dwi_file2}

Now the slurm output does not show any error but has created temporary files. so what is the reason and how do i get my output file?

what is wrong with this algo because

2

Hi @New,

OK, first off, we’ll need to clarify the issue:

  • you provide the -rpe_none option, which means you can’t or won’t do distortion correction, but then you also provide the reversed PE data via the -se_epi, which only really make sense if you use the -rpe_pair option. I doubt this is what is causing the issue, but given that it is unexpected usage, it’s not something that would necessarily have been tested extensively, so it could that simple…

  • what system is this on? What OS? What version of the OS? Is it running directly on the hardware, via a virtual machine, or some other container?

  • what version of MRtrix are you running?

  • You mention slurm, but I don’t see any suggestion that you’re using it in your code. If this is a slurm script, I’d expect to see a few more parameters somewhere.

  • you mention it created temporary files. What files exactly? The tmp folder? Or something else? Did it place that folder in the expected location? If it is the tmp folder, you should be able to inspect the logs contained within that folder, they may provide a hint.

  • What is the full slurm log output? Can you post its full contents here?

Hopefully some of this information will provide some clues as to what’s going on.
All the best,

Donald.