Matt Cieslak

We don't have a standalone cli tool for shoreline, but if you've worked with nipype before you should be able to get shoreline run on your mouse data. Let me...

@dubergonzoni any success with @pcamach2's suggestions?

you can also see a lot more printed out if you add -v flags. I usually run it with -v -v

your approach here should work. Try setting --nthreads 23 --omp-nthreads 22 and you will see better performance if you're running this on a single subject

I wonder if you're running out of memory. Just to be sure could you try --nthreads 8 --omp-nthreads 7? You may also want to add --skip-odf-reports

Thanks, this is definitely a bug

This looks awesome - I'm not going to be able to code for the next few weeks, so I'll add write access for you on this repo

> As well as the bvecs, what to do about the phase encoding directions for topup in the presence of rotation of the FOV? It's possible, though I've never seen...

There are a couple `tck2connectome` calls, each with a different weighting. For mean FA you probably don't want `-scale_length` and would want `-stat_edge mean`

@smeisler you're using HCP minimally preprocessed data as the input? there may be some issues with this because they write LAS+ results which can cause issues with how QSIPrep interprets...