Hi @jruizfdez,
Please provide more information about your QSIPrep command (e.g., as if you were making a new software support post).
Please also provide the tree directory structure of one subject’s QSIPrep outputs. Also note that QSIPrep does not have nested derivatives folders, only QSIRecon (since each postprocessing workflow is a different derivative dataset produced by QSIRecon).
You can see if any errors were encountered in the output html and/or runtime logs (e.g., SLURM .out/.err files).
Best,
Steven