fmriprep-apply CLI tool

[effigies]

Given an input directory and an output directory, generate a new output directory that applies all the relevant transforms found in the output directory to the images in the input directory. Unclear how much we want to validate that inputs match outputs in terms of metadata (e.g., RepetitionTime), but there should be a mode to disable any checks that are not absolutely necessary.

Part of #2207.

[Lestropie]

Note that not all transformations necessary to generate the output data will be pre-calculated and available in the existing BIDS Derivatives fmriprep directory. Eg. slice timing correction will need to be re-processed.

[Lestropie]

After an initial attempt at this, I decided that implementing and maintaining a stand-alone command for performing this reconstruction would be cumbersome. I am instead focusing on having a command-line option to the main fmriprep executable that regenerates the output fMRI data based on a prior fMRIPrep execution, re-computing only what needs to be re-computed and pulling data from the existing output derivatives directory where relevant.

[effigies]

This should be doable with --derivatives minimal=$prerun