Any actual windows paths had \, but the binding paths and fmriprep inputs had /
for example E:\my\host\path:/data blah blah fmriprep /data /output
I don’t know why this is not working. But can you try entering the docker container in an interactive shell (while mounting the paths) and seeing if the directories show up as expected? Try following something like this (but with additionally mounting the paths): Getting Into a Docker Container’s Shell | Baeldung
I’ve tried my best but here’s another stacked set of images. First I tried to run my container exactly as in that example you linked, but the container doesn’t show as running afterward. The second picture shows when I tried to run it directly from the Docker app, it runs and then exits almost immediately with the error you see at the bottom, that it needs arguments to run. The next image is me trying to run it from the command line with the standard binding method, doesn’t work. The final image was your other idea to just bind the main directory and give full paths to the bids and output, that also didn’t work. Long story short, I have no idea how to get this container running.
Not a direct solution to your problem, but have you considered using brainlife.io to process your data?
I’ll definitely look into it.
When I used the win system, I also encountered similar problems. So I bought a Mac computer, and the problem didn’t appear again. I consider that the path of some root files may be introduced in different ways.