Im not sure I follow what you mean when you say "the file convert into a text file." The FREESURFER_HOME/mni/bin/nu_correct file is a text file (its a script). Try making sure that it is still executable:

$> chmod a+x $FREESURFER_HOME/mni/bin/nu_correct

On 12/02/2016 02:31 PM, jean-simon.boucher.1@ens.etsmtl.ca wrote:

Hi Zeke,

I'm trying to make modification on the first line of nu_correct (perl file) and when I do the modification the file convert into a text file. I've tried to run freesurfer with the text file but I got a message of nu_correct command not found at the begining of the process.

Do you have an idea how to bypass the conversion perl to text file?

Thanks for your help!

Jean-Simon Boucher B. Ing. Électrique (ÉTS)

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De : freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] de la part de Z K [zkaufman@nmr.mgh.harvard.edu] Envoyé : 30 novembre 2016 15:39 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] TR : recon-all exited with ERRORS in Talairach

Hello Jean-Simon,

If indeed you are running the same subject on the same machine, then the reason its failing has to be because of an update to perl. It's possible your Linux update also updated the version of perl, even if only a minor verion update, and this is what created the issue. You have two solutions to using for using freesurfer at this point...

1. Update your version of freesurfer to the v6-beta release which fixes

the issue (the official v6 should be released in just a matter of 1-2).

2. Install perlbrew and use that to install perl version 5.20.3

   $> sudo apt-get install perlbrew $> perlbrew install perl-5.20.3

You then must change the first line of any mni script that fails (their should only be a few) to point to the perl v5.20 instead of the default. So for example, the first line of $FREESURFER_HOME/mni/bin/nu_correct should be changed from:

  #!/usr/bin/perl -w

to: #!~/perl5/perlbrew/perls/perl-5.20.3/bin/perl -w

You may need to do this with a couple of the MNI scripts. I know this is not an ideal solution but it is the only way I know of to get freesurfer5.3 working on platforms with perl 5.22

-Zeke

On 11/30/2016 02:51 PM, jean-simon.boucher.1@ens.etsmtl.ca wrote:

...

Hi Freesurfer Developpers,

I'm trying to ''recon-all'' my MRI and I got an error in Talairach parts of the process. This is strange because I was able to complete the process entirely few weeks ago ...

Here are the recon-all log files for the same subjects (the good one (few weeks ago) and the new one that I got now with ERROR). I've compared the 2 files and the only thing that is different is my platformversion (this is the linux version, right?). It has increased from 4.4.0.38 to 4.4.0.47.

The only things that I have changed since the first time that I was able to perform the freesurfer process are:

• Update on Linux
• Installation of a new hard drive. Note here that I've tried to bypass (not using) the hard drive in my process.

I've tried a lot of thing and one things that seem to be my problem is the Version of Perl (5.22.1) with my version of Freesurfer (5.3.0). (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-November/048807....) Strangely, I haven't upgraded any of theses since the first time that I was able to run Freesurfer. Moreover, I don't have the access to change the version of perl (yes I've tried to change it for version 5.16)

Do you have any idea what I'm doing wrong?

Thanks a lot!

Jean-Simon Boucher B. Ing. Électrique (ÉTS)

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