Error with 'Low Disk Space on "Filesystem root"' when running fmriprep on a VM in Ubuntu

I am running fmriprep on a virtual machine in Ubuntu 20.04.2 LTS. I have allotted 16GB RAM, 12 processors, and 50GB hard disk space to the VM. I have successfully ran it once before on a single dataset. I am now trying to run it again with a new dataset.

After running for some time, I get a notification from Ubuntu that there is ‘Low Disk Space on "Filesystem root’. Then, fmriprep throws some errors that it cannot find certain folders needed to continue running; however, fmriprep does not break when the error occurs. I assume it continues looking for the folder (?).

I have ran sudo baobab to assess the storage.
I have completely emptied my trash bin and emptied the cache (and cache trash) from the home/root. This did not seem to solve the issue. I am now looking into the Filesystem root where I see FSL and docker take up quite some storage.

Has anyone encountered this issue before or might there be some work around solution?

Attached is an image of the data analyzer.