Check if required inputs exist in pipeline.sh

[jakepalmer]

Added a check for existence of required inputs to pipeline.sh based on required input in README and assuming directory structure of docker/singularity.

Currently, if the b0 input doesn't match exactly b0.nii.gz then the pipeline will only fail after working for a while on the T1.nii.gz, with the prepare_input.sh script still indicating the b0.nii.gz input exists.

Discovered this when an upstream process named the b0 input as b0_tmp.nii.gz rather than b0.nii.gz. Intended that these checks catch this type of oversight early.

Note: I ran dos2unix to test this locally via docker, and unix2dos before commit.

(This is my first PR so I'm open to feedback!)

[baxpr]

@jakepalmer Awesome, thank you! This looks perfect to me but I will leave it up to the bosses @schillkg @hanscol to make final decision/merge when they get a chance.