Dear FreeSurfer team,

I am trying to run recon -all -autorecon2 using the following command line:  recon-all -sd ~/Desktop/MS_STUDY/subjects -s 001 -i /home/rosalia/Desktop/MS_STUDY/subjects/001 -autorecon2

 It is the same command I used yesterday to run -autorecon1 without problems. However, maybe now it is different. Should I point to another sub folder? I do not know which -i I should point out now. My directory for this subject is as follows:

rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $ ls
brainmask.auto.mgz          nu.mgz       rawavg.mgz
brainmask.mgz               orig         T1.mgz
mri_nu_correct.mni.log      orig.mgz     talairach_with_skull.log
mri_nu_correct.mni.log.bak  orig_nu.mgz  transforms
rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/MS_STUDY/subjects/001/mri $

Best regards,

Rosalia