fMRIprep container instructions need extensive improvement

[gdevenyi]

The installation instructions for containerized installation STRONGLY RECOMMEND using a container, and then provide no instructions to install it.

If you follow the links to the nipreps page, there is no copy-and-paste install command to use, versions available for fRMIprep are unknown.

I strongly recommend taking inspiration from cpac, which has a quickstart pip install wrapper, which will then pull, manage, and wrap container calls
https://fcp-indi.github.io/docs/latest/user/quick

[gdevenyi]

As a bare minimum of hackery, here's an adaptation of a wrapper I use to make a singularity container act like a normal command, it has limitations, in particular, it only exposes files in the run directory inside the container. I add this file to the same directory as the container, call it fmriprep and make it executable.

#!/bin/bash
set -euo pipefail

# Detect the directory of the script
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
# Pass the command line into the container file in the same directory
singularity run -B $(pwd):/mnt --pwd /mnt --cleanenv ${DIR}/fmriprep-20.2.6.simg $@