Hello Teodora,

In version 5.3 of freesurfer, The Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher). This is due to an incompatibility with the mni tools shipped with FreeSurfer v5.3 and newer versions of perl. The issue has been fixed the latest release of freesurfer v6.

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

-Zeke

On 02/22/2017 09:08 AM, teodora petrova wrote:

Hello Freesurfer Developers,

I have tried a manual Talairach alignment, according to this tutorial: http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview . But when I run the command

recon-all -all -subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 , the run stops at the following step:

#-------------------------------------------- #@# Talairach tor 16 feb 2017 11:09:05 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri

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

Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at tor 16 feb 2017 11:09:08 CET

I have searched in the support archives, but I did not find a complete solution of the problem in none of the threads.

1. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2. Platform: Ubuntu MATE 16.04
3. see recon-all.log attached

Thank you for your help.

Best, Teodora

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