-force flag on proc_dwi deletes proc_structural through post_structural output

[ajschadler12]

• What is the current behavior?
  • Run proc_structural, proc_surf, post_structural, and proc_dwi with -force flag. proc_dwi failes because it overwrites subject output with empty directories.
• Please provide the steps to reproduce and if possible a minimal demo of the problem
  • Run proc_structural through post_structural then proc_dwi, all with -force flag. Structural processing will not delete output.
• What is the expected behavior?
  • proc_dwi with -force flag should only overwrite diffusion output.
• Please tell us about your computing environment:
  • Linux.
  • Container: singularity built from v0.2.1 docker container.

[rcruces]

Hello,

Indeed the -force flag is not specific per module. When you use it it will erase all the subject's directory and re-process everything. If for any reason you would like to erase a specific module before re-runing the option -cleanup is the one that will erase it.

If you want to erase a module created by proc_dwi use the following flags: micapipe -sub <SUB> -ses <SES> -cleanup -acqStr <DWI-NAME> -proc_dwi

It's a good observation that the option force should overwrite the module. We'll keep it in mind for future implementations.