For the input,I try using this command:
# recon-all -s $MY_SUBJECT -i $SUBJECT_DIR/$MY_SUBJECT/mri/ orig/sujet01.nii.gz -all -notal-check -no-isrunning
It returns the following error:
# ERROR: /home/christophe/con/dvlp/pipe/FS/subjects/sujet01 exists, delete or re-run with -force
...