Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl v5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer and that version of perl. The issue has been fixed in the development version of FreeSurfer.

The only work around is to either downgrade to the previous version of perl (5.18), or use the development version of freesurfer which can be downloaded via the following link:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

-Zeke

On 07/08/2016 08:49 AM, Emeline MULLIER wrote:

Hello FreeSurfer Developers,

I have just tried to install FreeSurfer on a new machine and I met a problem with recon-all command.

I have tried the tutorial command : recon-all -s bert -all And I have the error message : recon-all -s bert exited with ERRORS.

My machine is on Ubuntu 16.04. I installed : freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 I attached my recon-all.log. $FREESURFER_HOME /usr/local/freesurfer

I saw a similar problem with virtualbox shared folder but it is not my case here.

Do you have an idea of the problem ?

Thank you,

__

Emeline MULLIER PhD Candidate

Department of Radiology Center hospitalier universitaire vaudois (CHUV) and Université de Lausanne (UNIL) Rue du Bugnon 46, CH-1011

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer