Option 1:

Yacilita:subjects Yacilita$ mri_convert sample-001.mgz sample-001.nii.gz
mri_convert.bin sample-001.mgz sample-001.nii.gz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from sample-001.mgz...
TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
i_ras = (-0, -1, -0)
j_ras = (-0, 0, -1)
k_ras = (-1, 0, 0)
writing to sample-001.nii.gz...
Yacilita:subjects Yacilita$ recon-all -i sample-001.nii.gz -s bert -all
if: Missing file name.
Yacilita:subjects Yacilita$ 

Option 2:

Yacilita:freesurfer Yacilita$ cd /Volumes/Yacila/data/DZNE/Freesurfer/
Yacilita:Freesurfer Yacilita$ export SUBJECTS_DIR=</Volumes/Yacila/data/DZNE/Freesurfer
Yacilita:Freesurfer Yacilita$ recon-all -i 907_03 -s bert -all
907_03T2_highres.nii.gz    907_03_T1_standard.nii.gz  907_03_T2standard.nii.gz   907_03_oT2.nii.gz          
Yacilita:Freesurfer Yacilita$ recon-all -i 907_03_T1_standard.nii.gz -s bert -all
if: Missing file name.