I am a student learning FreeSurfer and attempting to compute cortical volume and other brain structural measurements for my subjects. So I ran recon-all on several subjects and the sample subjects converted from FreeSurfer installation tutorial. The first step for recon-all did not exit with errors (command line: recon-all -s sample-001 -i /home/zqn/freesurfer/subjects/sample-001.nii.gz). 

But I got the following error when I ran the second step for recon-all (command line: recon-all -s sample-001 -all):

I cannot find out what the error is and the way to solve it.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

2) Platform: Ubuntu 18.04

3) recon-all.log: see attached

Hope to hear from you soon.

Thanks,

Sincerely,

Qiannan