SDC and Fmap JSON Requirements

[toomanycats]

Fieldmaps and SDC Getting the SDC to work has been a challenge.

Quote from Doc: "Please note that all routines for susceptibility-derived distortion correction have been excised off of fMRIPrep for utilization on other projects (e.g., dMRIPrep)."

I read that to mean, SDC was no longer performed in fmriPrep. Then I realized that was unlikely, and that I needed another library. Then after looking through the source code decided that I was still wrong and SDC is performed and included.

Suggestion: "Please note that all routines for susceptibility-derived distortion correction have been moved into their own code base sdcflows. Their documentation can be found at ".

B0FieldSource In addition it's unclear which fieldmap side cars files need the "B0FieldSource" key-value. The way I read the BIDS spec v1.7.0 (page 98 PDF), is that only the phasediff image required that meta data.

Suggestion: Add a paragraph to explicitly state which files get the key-value pairs.

Missing doc for Nipype runtime options I ran into an issue which looks like an NFS bug with the SQLITE sqlalchemy driver. It was suggested to use the option --bids-database-dir which worked out really well. I went looking for this option and I never found it documented. I suspect it is a Nipype option.

Suggestion: In the Usage section with args and flags, link to any other Nipype documentation on flags that can be passed down.

I'm happy to fork the doc if that helps and attempt to add details myself if that's helpful.

[effigies]

We'd definitely appreciate docs suggestions from someone with a fresh eye! Please feel free to submit a PR.