Matt Cieslak

Are you running this via docker or singularity? I wonder if the nipype config isn't visible inside the container

I've actually never seen a docker service being used for qsiprep. What happens if you mount the config file at `/root/.nipype/nipype.cfg`?

It looks like you can set where nipype will look for the config file with the [`NIPYPE_CONFIG_DIR`](https://github.com/nipy/nipype/blob/28d424f5dda3a23b01227379d91a825b0932efae/nipype/utils/config.py#L94) environment variable. If you set this in your container and mount the config...

This was fixed in 0.17 and can be selected with the --denoised_image_sdc flag

It's been much more than a year now, but I might suggest it's not a good idea to combine single and multishell data into a single processing stream.

this is a very old issue, please reopen if you're still having trouble or would like to revisit

This is worth adding to the documentation

Is sounds like the assignments.txt is a file that would be useful to add to the derivatives?

@vnckppl which version of qsiprep are you using? As of 0.16.0 there is a connectome2tck results directory included in the mrtrix outputs

they're archived in `sub-TEST_space-T1w_desc-preproc_desc-exemplarbundles_dhollanderconnectome.zip`!