T1-FreeSurfer requires interaction

[MatthieuJoulot]

Hi Clinica devs,

I have been using t1-freesurfer these days, and it turns out, it is not possible to launch a batch job if your images are not centered, because, t1-freesurfer is interactive when it is the case. It asks whether you want to continue launching t1-freesurfer. Which I can't since it is a slurm job.

This behavior is linked to a usage of t1-freesurfer which is not just something your average Joe does.

I think there is different approaches to handle this:

1. Give warnings in t1-freesurfer.
2. Have a pet-surface flag which would ensure a centered dataset is used, as you may hope that your advanced Joe would have read the different documentations and therefore know about the centering.
3. Be explicit about it in the --help documentation

Have a good one and see you soon 😘
Matthieu