[root@localhost ~]# cp $FREESURFER_HOME/subjects/sample-001.mgz .
cp: cannot stat `/subjects/sample-001.mgz': No such file or directory
[root@localhost ~]# $> cp $FREESURFER_HOME/subjects/sample-001.mgz .
bash: $: command not found
[root@localhost ~]# > cp $FREESURFER_HOME/subjects/sample-001.mgz .
bash: /subjects/sample-001.mgz: No such file or directory
[root@localhost ~]# cp $FREESURFER_HOME/subjects/sample-001.mgz
cp: missing destination file operand after `/subjects/sample-001.mgz'
Try `cp --help' for more information.
[root@localhost ~]# export FREESURFER_HOME=/usr/local/freesurfer
[root@localhost ~]# source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
[root@localhost ~]# export SUBJECTS_DIR=/usr/local/freesurfer/subjects
[root@localhost ~]# cp $FREESURFER_HOME/subjects/sample-001.mgz .
cp: overwrite `./sample-001.mgz'? y
[root@localhost ~]# 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...
[root@localhost ~]# export SUBJECTS_DIR=FREESURFER_HOME/subjects/sample-001.mgz .
bash: export: `.': not a valid identifier
[root@localhost ~]# export SUBJECTS_DIR=$FREESURFER_HOME/subjects/sample-001.mgz .
bash: export: `.': not a valid identifier
[root@localhost ~]# export SUBJECTS_DIR=/root/sample-001.nii.gz
[root@localhost ~]# recon-all -i sample-001.nii.gz -s bert -all
/root/sample-001.nii.gz: Not a directory.
[root@localhost ~]#