Running fmriprep on PC


I have a dual-boot system on my personal computer between windows and linux and I was wondering which OS I should use for fmriprep. I’m more used to Windows, so I’d like to install it there, but it seems like fmriprep has several external dependencies (like FSL among others) that can’t easily be installed on Windows. I haven’t installed fmriprep yet but I couldn’t find any information about how the external dependencies are managed. Do all of the programs on the external dependency list need to be installed and running in order to use fmriprep? (this would mean I should use linux)

FMRIPREP comes bundle with all of the dependencies it needs, so you don’t need to install FSL or other neuroimaging software. This bundling is possible due to software called Docker which is the only FMRIPREP dependency you need to install. More info at

Docker works on Linux, Windows, and Mac. There are some differences in terms of how it works on Windows vs Linux. Most notably I/O (reading writing from disk) is a little bit faster on Linux.

Oh awesome! This is great!
I think I didn’t realize that the ‘external dependencies’ section is a subheading under manually prepared environment… I thought it was its own heading…
Thank you very much!