Hello Albert,

The centos4 vs centos6 output you are seeing is not the problem. Log files get appended to (unless you use the -noappend option), so you'll actually see the proper FREESURFER_HOME value your expecting later in the file.

The issue is that the version of the MNI tools shipped with freesurfer use a version of perl that is incompatible with the version of perl shipped with the latest linux distribution. To fix this problem you can use the development version of freesurfer available for download from this page (see "Development Version"):

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall

This issue will also be resolved in the upcoming release.

-Zeke

On 11/01/2016 05:35 AM, Lehr, Albert wrote:

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

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