Hi Nick,
Thanks for your help. I'm running v4.5.0 on our cluster. I'm don't think the latest version has been installed. I might just ask them to install v5.2. Should I re-run the recon_all steps again with this latest version? Should I disregard the results that have already been computed with this error? I am still a Freesurfer beginner unfortunately so apologies for asking such questions!
Thanks again,
Sinead
On 4 March 2013 14:50, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:
Sinead
Are you running v5.0.0? This link has some info on fixing the problem, something your admin will have to do:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-December/012846....
Or better yet you can them install install v5.2, which doesnt have that dependency in mris_volmask:
https://surfer.nmr.mgh.harvard.edu/fswiki/Download
Nick
Dear members,
I am currently conducting cortical thickness analysis and I have ran the recon_all step. The appropriate files have been created including aseg.mgz, brainmask.mgz, aseg.stats etc. and therefore volumes and cortical thickness measures have been calculated, however, when I look at the output of my script it states that the job has exited with errors (see below)
mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 001
mris_volmask.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory Linux tcin-n05.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Mar 1 20:00:42 GMT 2013
I'm not too sure what the error is or how to fix it. However, as the relevant files have been created, should I be too concerned about this? Also, I should mention that I am running my scripts on a high performance computing cluster and not locally on my linux.
Thank you for your help!
Sinead
-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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