Dear FreeSurfers,

I just recently installed FreeSurfer and as Saeed ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49263.html) had troubles  running recon-all.

My info:
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Linux version: Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

I attach my recon-all.log but I guess it is very similar to Saeed's. Also running

mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50   --no-rescale --i orig.mgz --o orig_nu.mgz

gives the exact output and error code as he had. I already read that downloading the Development Version should get the job done, but noticed some stuff and wanted to ask about it:

Running "recon-all -s bert -all" , the following lines are shown and the build stamps do not match.

INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/bin/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/bin/freesurfer
-rw-r--r-- 1 albert albert 513977 Oct 31 16:30 /usr/local/bin/freesurfer/subjects/bert/scripts/recon-all.log
Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
    Current: /usr/local/bin/freesurfer
    Previous: /space/freesurfer/centos4.0/stable


Equally in the attached recon-all.log file
"FREESURFER_HOME /space/freesurfer/centos4.0/stable
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0/stable5"

is written and although I downloaded the centos6-version and not the centos4.0 version. Might this be a problem or is the error solely due to the new perl versions? Just wanted to bring it to your attention and hear your feedback. I am currently downloading the 6.0.0-beta version, which hopefully makes recon-all work again.

Have a great day,

Albert