Matt Cieslak

Definitely open for a PR on this one. It should be really easy to reorient the T1ws since they don't have and extra orientation-dependent data

For the record this is the default setting for eddy, not something unique to qsiprep. You can find the eddy info in the `desc-SliceQC_dwi.json` file in the results.

It sounds like something crashed during your run before the figures were created. Were you also running reconstruction workflows?

I think there might be something going on with the 3 positional arguments that have to be specified `bids_dir output_dir participant` In your command I'm only seeing `/Shared//BIDS/derivatives participant`

@giulia-berto are you using the `--output-spaces template` argument?

You can specify a text file as an argument to `--bids-filter-file` that selects for the session you want to process. There is some documentation we're failing to get on readthedocs...

Hi! I suggest using --dwi-only and doing all your infant-specific anatomical work outside of qsiprep. The T1w-based registration is good for getting gray matter atlases into alignment with the DWIs,...

@36000

Hi @treanus, we haven't optimized the user setup for docker since singularity is much more common. Until we have a good fix for this, I think you can `docker run...

how different are the parameters between the scans? Are there other things that vary other than the b-value in the 3 scans? Also, which version of qsiprep are you using?