Center nifti does not work how it is supposed to

[MatthieuJoulot]

Dear Clinica devs,

Following my unsuccessful usage of t1-freesurfer, I used center-nifti which does not work the way it says it does. The help section says that the mandatory arguments are a bids_directory and an output_directory. However if an additional argument is not given, whether it is -m/--modality or --center-all-files nothing is done.

It looks like there are two options:

1. remove the --center-all-files flag and make processing all files the default behavior (which is what I thought it would do).
2. make an other compulsory argument to say whether all the files or only selected modalities should be processed (which seems counter-intuitive and complicated to implement cleanly IMHO)

Have a good one,
Matthieu