I also see this error which is sent to stderr:

/usr/bin/time: cannot run recon-all: No such file or directory

It seems to be something related to the time command (or bash keyword)

Is your Freesurfer Environment sourced correctly?  Here is the wiki
help 
https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNgMM75HegbbUkTZoxL85vJjghWDwtg3Jjv4lsG0VZCTZ7YlhPuRczAQuIz8jePrWEIPQwVyAzcYv98U1CgmMpRUs3NZobucvYycgHFiqQk2sbCWslDa4-IfTbm2n-MTOjXS2Ej1uEpNgZ9lfvkJzcnj7SR5NRRe89nzPhY3jV3X1RPryu31aaVnBfDV7xeQ-b5WO6aR70li-RGAhVttoiUOo_E_Pj4-motaxaqZfNAhXYFAezM4dVSZlRAPrkwuMJG-Op02Vd54RwqKG-0U9qMFpYXqv7SLkSpIzyjUtjEw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing