External Email - Use Caution        


The best solution (which I think was previously emailed to you) is to have an admin/IT person update your system by doing the following:

1) Copy the link for the freesurfer release install package matching your Ubuntu system, e.g., 7.3.2 freesurfer release on Ubuntu 18, 20, 22, from
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

2) Download and install it with,

$ wget <link copied from the web page above>
.... say wget downloaded the file freesurfer_ubuntu18-7.3.2_amd64.deb  ....
$ sudo apt-get install ./freesurfer_ubuntu18-7.3.2_amd64.deb

That should install libncurses and anything else that's needed automatically.   Trying to piecemeal run commands to install individual system packages like libncurses is asking for more trouble.

- R.

On 2/22/23 10:54, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ@mgh.harvard.edu) wrote:

Thanks for the interest in our software!

Could you please try running this command from the terminal?

sudo apt-get install libncurses5

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of behçet ayyıldız <behcetayyildizz@gmail.com>
Reply-To: Freesurfer support list <Freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, February 15, 2023 at 05:36
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] segmenThalamicNuclei.sh exited with ERRORS

 

        External Email - Use Caution        

Dear All, 

I was using Linux Ubuntu to perform my analysis. However, they were changed with Linux ..... a couple of days ago. And while the segmentThalamicNuclei.sh command was running before the change, after the change it didn't run and I got the following message.

 

 

drodriguez@causal:/data_august/Daniela/Behcet/Freesurfer_pulvinar_OCD$ segmentThalamicNuclei.sh con_HaJa93

Setting ITK threads to 1

#--------------------------------------------

#@# Thalamic Nuclei processing Wed 15 Feb 2023 11:09:10 AM CET

------------------------------------------

Setting up environment variables

---

LD_LIBRARY_PATH is ..:/sw/freesurfer/7.1.1//MCRv84//runtime/glnxa64:/sw/freesurfer/7.1.1//MCRv84//bin/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/os/glnxa64:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sw/freesurfer/7.1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sw/freesurfer/7..1.1//MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:

/sw/freesurfer/7.1.1//bin/SegmentThalamicNuclei: error while loading shared libraries: libncurses.so.5: cannot open shared object file: No such file or directory

127

Linux causal.brain.mri.tu-muenchen.de 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux

 

Do you guys have any idea how to fix it ?

 

Thanks in advance.

 

--

Behçet Ayyıldız..


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