Matt Cieslak

How about the quality of the results? I don't think the actual processing will be that different, but you'll have a much more difficult time getting the alternative templates into...

Any of those should be ok

The readthedocs error is very strange, I don't think this PR changes anything in extras_require

I think this will work, but I'm wondering if we should hold off on major refactors until we add a couple more CI tests (like for GRE fieldmaps). Wdyt?

In our case there were two subjects that had the same ID but with different capitalization (sub-ndar, sub-NDAR) in the root bids directory. All the files within their directories matched...

@jhauneuro and @johnaeanderson do you see cropping in the preprocessed images too? Or is it just in the figure?

Hi @jhauneuro are you sure your data is bids valid and does it contain SliceTiming? We added the slice-to-volume correction in these recent versions, which will look at your slice...

oh, that's unfortunate. Maybe the best approach would be to implement `--output-resolution auto`

> I also have a different eddy config file for each dwi sequence to set the `mporder` parameter. I calculate that manually as per FSL guidelines (N/4 to N/2; N=number...

I've never run into PSR dwi data before, so it's possible there is something missing in the workflow that reads in the images. Would you be able to share some...