MRTRIX preprocessing issue

Apologies - I am new to imaging analysis and all these software.

I am trying to go down the pipeline to generate tractography for a batch of 14 DTI images for patients.

While trying to run dwifslpreproc my code seems to get stuck at
Command: eddy --imain=eddy_in.nii --mask=eddy_mask.nii --acqp=eddy_config.txt --index=eddy_indices.txt --bvecs=bvecs --bvals=bvals --out=dwi_post_eddy --verbose

I know this preprocessing stage can take many hours and so I left it overnight but it still was stuck at the same time.

This is the code I am running (I do not have PA images, so only working with AP):
$ dwifslpreproc PT1_preop_DTIden.mif PT1_preop_DTIden_preproc.mif -rpe_none -pe_dir ap -readout_time 0.044856

Could anyone suggest a solution for this please?

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Welcome @SanskrithiS!

It’s very difficult to diagnose anything from this information alone, given that it’s a pretty simple use case and there’s no real hints.
What I would suggest is:

  1. Re-run dwifslpreproc, specifying the -nocleanup option.
  2. Once the eddy command commences, Ctrl-C to kill the script.
  3. Navigate into the scratch directory left behind by dwifslpreproc.
  4. Manually check all of the prepared inputs to eddy to make sure they are sensible.
  5. Manually execute the quoted eddy command.

Maybe it will generate some information at the terminal that will be of use.