Passing fmriprep arguments to fmriprep-docker wrapper

docker
fmriprep

#1

Hi,

Tis might seem like an obvious question but I haven’t found any information about it in the documentation. I’m using the fmriprep-docker wrapper to run fmriprep. I’d like to pass the --use-syn-sdc argument. How do I pass low-level input args for fmriprep into fmriprep-docker? Many thanks.


#2

Just put them at the end of your command line.


#3

Actually- when typing fmriprep-docker -h- one finds that all of the options are supported, though in the website documentation- only a small subset is shown to be supported- it seems as if the documentation website should be updated.
Thanks


#4

Thanks, your suggestion was noted here - https://github.com/poldracklab/fmriprep/issues/1129